| algeria | | cryptosporidium sp. hedgehog genotype | species | 8 | 0 |
| australia | | cryptosporidium sp. deer genotype | species | 1 | 0 |
| australia | | cryptosporidium sp. duck-like genotype | species | 1 | 0 |
| australia | | cryptosporidium sp. genotype mw1 | species | 1 | 0 |
| australia | | cryptosporidium sp. genotype mw2 | species | 1 | 0 |
| australia | | cryptosporidium sp. genotype mw3 | species | 1 | 0 |
| australia | | cryptosporidium sp. genotype mw4 | species | 1 | 0 |
| australia | | cryptosporidium sp. genotype mw5 | species | 1 | 0 |
| australia | | cryptosporidium sp. genotype mw6 | species | 1 | 0 |
| australia | | cryptosporidium sp. genotype rta368 | species | 1 | 0 |
| australia | | cryptosporidium sp. marsupial genotype ii | species | 1 | 0 |
| australia | | cryptosporidium sp. mink genotype | species | 1 | 0 |
| australia | | cryptosporidium sp. piscine genotype 4 | species | 1 | 0 |
| australia | | cryptosporidium sp. piscine genotype 5 | species | 1 | 0 |
| australia | | cryptosporidium sp. rat/ap-2012/gii | no rank | 6 | 0 |
| australia | | cryptosporidium sp. rat/ap-2012/giii | no rank | 4 | 0 |
| australia | | cryptosporidium sp. sheep genotype i | species | 2 | 0 |
| australia | new south wales | cryptosporidium sp. deer genotype | species | 2 | 0 |
| australia | new south wales | cryptosporidium sp. duck-like genotype | species | 2 | 0 |
| australia | queensland | cryptosporidium sp. mink genotype | species | 2 | 0 |
| australia | victoria | cryptosporidium sp. genotype 1 | species | 1 | 0 |
| australia | victoria | cryptosporidium sp. genotype 2 | species | 1 | 0 |
| australia | victoria | cryptosporidium sp. genotype 3 | species | 1 | 0 |
| bangladesh | | cryptosporidium sp. horse genotype | species | 1 | 0 |
| belgium | | cryptosporidium sp. horse genotype | species | 3 | 0 |
| brazil | | cryptosporidium sp. avian genotype iii | species | 5 | 0 |
| brazil | | cryptosporidium sp. avian genotype v | species | 1 | 0 |
| brazil | | cryptosporidium sp. hamster genotype | species | 1 | 0 |
| brazil | | cryptosporidium sp. pig/h4/bra/gii | species | 1 | 0 |
| brazil | | cryptosporidium sp. pig/i1/bra/gii | species | 1 | 0 |
| brazil | mato grosso do sul | cryptosporidium sp. deer genotype | species | 2 | 0 |
| brazil | parana | cryptosporidium sp. genotype brpr1 | species | 6 | 0 |
| canada | ontario | cryptosporidium sp. muskrat genotype i (w7) | species | 7 | 0 |
| canada | ontario | cryptosporidium sp. muskrat genotype ii (w16) | species | 8 | 0 |
| canada | ontario | cryptosporidium sp. shrew genotype (w5) | species | 1 | 0 |
| china | | cryptosporidium sp. avian genotype ii | species | 2 | 0 |
| china | | cryptosporidium sp. avian genotype v | species | 3 | 0 |
| china | | cryptosporidium sp. cervine genotype | species | 66 | 0 |
| china | | cryptosporidium sp. chipmunk genotype iii | species | 2 | 0 |
| china | | cryptosporidium sp. deer genotype | species | 13 | 0 |
| china | | cryptosporidium sp. donkey genotype | species | 2 | 0 |
| china | | cryptosporidium sp. ferret genotype | species | 3 | 0 |
| china | | cryptosporidium sp. giant panda genotype | species | 1 | 0 |
| china | | cryptosporidium sp. ground squirrel genotype ii | species | 3 | 0 |
| china | | cryptosporidium sp. hamster genotype | species | 1 | 0 |
| china | | cryptosporidium sp. horse genotype | species | 8 | 0 |
| china | | cryptosporidium sp. mink genotype | species | 13 | 0 |
| china | | cryptosporidium sp. mouse genotype i | species | 2 | 0 |
| china | | cryptosporidium sp. pig genotype ii | species | 18 | 0 |
| china | | cryptosporidium sp. rat genotype ii | species | 2 | 0 |
| china | | cryptosporidium sp. rat genotype iii | species | 1 | 0 |
| china | | cryptosporidium sp. yak genotype | species | 1 | 0 |
| china | inner mongolia | cryptosporidium sp. horse genotype | species | 4 | 0 |
| china | shandong | cryptosporidium sp. horse genotype | species | 2 | 0 |
| china | shandong | cryptosporidium sp. mink genotype | species | 1 | 0 |
| china | xinjiang | cryptosporidium sp. horse genotype | species | 1 | 0 |
| czech republic | | cryptosporidium sp. bat genotype iv | species | 4 | 0 |
| czech republic | | cryptosporidium sp. deer genotype | species | 1 | 0 |
| czech republic | | cryptosporidium sp. hedgehog genotype | species | 3 | 0 |
| czech republic | | cryptosporidium sp. horse genotype | species | 2 | 0 |
| czech republic | | cryptosporidium sp. pig genotype ii | species | 1 | 0 |
| czech republic | | cryptosporidium sp. tortoise genotype iii | species | 2 | 0 |
| france | | cryptosporidium sp. cervine genotype | species | 1 | 0 |
| france | corse region | cryptosporidium sp. rat genotype ii | species | 6 | 0 |
| france | corse region | cryptosporidium sp. rat genotype iii | species | 1 | 0 |
| germany | | cryptosporidium sp. avian genotype ix | species | 1 | 0 |
| germany | | cryptosporidium sp. avian genotype vii | species | 1 | 0 |
| germany | | cryptosporidium sp. avian genotype viii | species | 1 | 0 |
| germany | | cryptosporidium sp. skunk genotype | species | 3 | 0 |
| india | | cryptosporidium sp. avian genotype iii | species | 1 | 0 |
| iran | | cryptosporidium sp. avian genotype iii | species | 14 | 0 |
| italy | | cryptosporidium sp. chipmunk genotype i | species | 7 | 0 |
| italy | | cryptosporidium sp. ferret genotype | species | 6 | 0 |
| italy | | cryptosporidium sp. horse genotype | species | 9 | 0 |
| italy | | cryptosporidium sp. skunk genotype | species | 3 | 0 |
| japan | aichi prefecture | cryptosporidium sp. ferret genotype | species | 1 | 0 |
| japan | hokkaido prefecture | cryptosporidium sp. deer genotype | species | 17 | 0 |
| japan | osaka prefecture | cryptosporidium sp. skunk genotype | species | 6 | 0 |
| japan | saitama prefecture | cryptosporidium sp. masked palm civet genotype | species | 3 | 0 |
| japan | saitama prefecture | cryptosporidium sp. skunk genotype | species | 1 | 0 |
| japan | saitama prefecture | cryptosporidium sp. skunk-like genotype | species | 3 | 0 |
| japan | tokyo prefecture | cryptosporidium sp. bah7 | species | 2 | 0 |
| japan | tokyo prefecture | cryptosporidium sp. horse genotype | species | 4 | 0 |
| kenya | | cryptosporidium sp. horse genotype | species | 4 | 0 |
| malaysia | | cryptosporidium sp. rat genotype ii | species | 5 | 0 |
| malaysia | | cryptosporidium sp. rat genotype iii | species | 1 | 0 |
| netherlands | | cryptosporidium sp. horse genotype | species | 1 | 0 |
| nigeria | oyo | cryptosporidium sp. rat genotype | species | 28 | 0 |
| norway | | cryptosporidium sp. cervine genotype | species | 3 | 0 |
| papua new guinea | | cryptosporidium sp. rat genotype ii | species | 1 | 0 |
| philippines | | cryptosporidium sp. bat genotype ii | species | 2 | 0 |
| philippines | | cryptosporidium sp. bat genotype v | species | 2 | 0 |
| philippines | | cryptosporidium sp. bat genotype vi | species | 3 | 0 |
| philippines | | cryptosporidium sp. bat genotype vii | species | 2 | 0 |
| poland | | cryptosporidium sp. horse genotype | species | 2 | 0 |
| poland | | cryptosporidium sp. skunk genotype | species | 2 | 0 |
| spain | | cryptosporidium sp. avian genotype iii | species | 3 | 0 |
| spain | | cryptosporidium sp. duck genotype b | species | 1 | 0 |
| spain | | cryptosporidium sp. goose genotype id | species | 1 | 0 |
| spain | canary islands | cryptosporidium sp. rat genotype ii | species | 7 | 0 |
| sri lanka | | cryptosporidium sp. genotype 10 | species | 1 | 0 |
| sri lanka | | cryptosporidium sp. genotype 11 | species | 1 | 0 |
| sri lanka | | cryptosporidium sp. genotype 4 | species | 1 | 0 |
| sri lanka | | cryptosporidium sp. genotype 5 | species | 1 | 0 |
| sri lanka | | cryptosporidium sp. genotype 6 | species | 1 | 0 |
| sri lanka | | cryptosporidium sp. genotype 7 | species | 1 | 0 |
| sri lanka | | cryptosporidium sp. genotype 8 | species | 1 | 0 |
| sri lanka | | cryptosporidium sp. genotype 9 | species | 1 | 0 |
| sweden | | cryptosporidium sp. chipmunk genotype i | species | 4 | 0 |
| sweden | | cryptosporidium sp. horse genotype | species | 1 | 0 |
| thailand | | cryptosporidium sp. mouse genotype | species | 3 | 0 |
| united kingdom | | cryptosporidium sp. cervine genotype | species | 5 | 0 |
| united kingdom | | cryptosporidium sp. horse genotype | species | 5 | 0 |
| united kingdom | | cryptosporidium sp. muskrat genotype ii | species | 1 | 0 |
| united kingdom | | cryptosporidium sp. rat genotype | species | 1 | 0 |
| united kingdom | | cryptosporidium sp. skunk genotype | species | 3 | 0 |
| united states | | cryptosporidium sp. 16008 | no rank | 2 | 0 |
| united states | | cryptosporidium sp. avian genotype iii | species | 1 | 0 |
| united states | | cryptosporidium sp. avian genotype v | species | 1 | 0 |
| united states | | cryptosporidium sp. avian genotype vi | species | 5 | 0 |
| united states | | cryptosporidium sp. bat genotype iii | species | 3 | 0 |
| united states | | cryptosporidium sp. cervine genotype | species | 1 | 0 |
| united states | | cryptosporidium sp. chipmunk genotype ii | species | 65 | 0 |
| united states | | cryptosporidium sp. chipmunk genotype iv | species | 5 | 0 |
| united states | | cryptosporidium sp. deer genotype | species | 1 | 0 |
| united states | | cryptosporidium sp. mink genotype | species | 1 | 0 |
| united states | | cryptosporidium sp. skunk genotype | species | 2 | 0 |
| united states | california | cryptosporidium sp. genotype sbey11c | species | 4 | 0 |
| united states | california | cryptosporidium sp. genotype sbey11e | species | 1 | 0 |
| united states | minnesota | cryptosporidium sp. deer mouse genotype iii | species | 10 | 0 |
| united states | minnesota | cryptosporidium sp. skunk genotype | species | 8 | 0 |
| united states | new york | cryptosporidium sp. beaver genotype | species | 1 | 0 |
| united states | new york | cryptosporidium sp. cervine genotype (w4) | species | 2 | 0 |
| united states | new york | cryptosporidium sp. chipmunk genotype (w17) | species | 1 | 0 |
| united states | new york | cryptosporidium sp. deer mouse genotype i | species | 3 | 0 |
| united states | new york | cryptosporidium sp. deer mouse genotype ii | species | 1 | 0 |
| united states | new york | cryptosporidium sp. deer mouse genotype iii (w1) | species | 1 | 0 |
| united states | new york | cryptosporidium sp. deer mouse genotype iv (w3) | species | 1 | 0 |
| united states | new york | cryptosporidium sp. goose genotype ii | species | 1 | 0 |
| united states | new york | cryptosporidium sp. mink genotype | species | 1 | 0 |
| united states | new york | cryptosporidium sp. muskrat genotype i (w7) | species | 3 | 0 |
| united states | new york | cryptosporidium sp. muskrat genotype ii (w16) | species | 1 | 0 |
| united states | new york | cryptosporidium sp. shrew genotype (w5) | species | 2 | 0 |
| united states | north dakota | cryptosporidium sp. ground squirrel genotype i | species | 10 | 0 |
| united states | north dakota | cryptosporidium sp. ground squirrel genotype ii | species | 2 | 0 |
| united states | north dakota | cryptosporidium sp. ground squirrel genotype iii | species | 14 | 0 |
| united states | vermont | cryptosporidium sp. chipmunk genotype i | species | 48 | 0 |