| lichtheimia corymbifera | 24 | species | plants | fungi | 42458 |
| ligula intestinalis | 22 | species | invertebrates | helminths | 94845 |
| listeria ivanovii | 32 | species | bacteria | bacteria | 1638 |
| listeria monocytogenes | 207 | species | bacteria | bacteria | 1639 |
| listeria seeligeri | 25 | species | bacteria | bacteria | 1640 |
| listeria welshimeri | 21 | species | bacteria | bacteria | 1643 |
| loa loa | 30 | species | invertebrates | helminths | 7209 |
| lomentospora prolificans | 44 | species | plants | fungi | 41688 |
| louping ill virus | 14 | species | viruses | viruses | 11086 |
| lymphocytic choriomeningitis mammarenavirus | 148 | species | viruses | viruses | 11623 |
| lysinibacillus sphaericus | 60 | species | bacteria | bacteria | 1421 |
| macacine herpesvirus 1 | 25 | species | viruses | viruses | 10325 |
| machupo mammarenavirus | 18 | species | viruses | viruses | 11628 |
| macracanthorhynchus hirudinaceus | 11 | species | | helminths | 1032456 |
| macracanthorhynchus ingens | 7 | species | invertebrates | helminths | 60534 |
| madrid virus | 1 | species | viruses | viruses | 348013 |
| madurella mycetomatis | 14 | species | plants | fungi | 100816 |
| malassezia furfur | 48 | species | plants | fungi | 55194 |
| malassezia globosa | 16 | species | plants | fungi | 76773 |
| malassezia obtusa | 4 | species | plants | fungi | 76774 |
| malassezia pachydermatis | 28 | species | plants | fungi | 77020 |
| malassezia restricta | 10 | species | plants | fungi | 76775 |
| malassezia slooffiae | 4 | species | plants | fungi | 76776 |
| malassezia sympodialis | 21 | species | plants | fungi | 76777 |
| mammomonogamus laryngeus | 2 | species | | helminths | |
| mammomonogamus nasicola | 1 | species | | helminths | |
| mannheimia haemolytica | 67 | species | bacteria | bacteria | 75985 |
| mansonella ozzardi | 17 | species | invertebrates | helminths | 122354 |
| mansonella perstans | 18 | species | invertebrates | helminths | 42231 |
| mansonella rodhaini | -3 | species | | helminths | |
| mansonella semiclarum | -3 | species | | helminths | |
| mansonella streptocerca | 5 | species | | helminths | |
| marburgvirus | 23 | genus | viruses | | 186537 |
| marituba virus | 5 | species | viruses | viruses | 292278 |
| marshallagia marshalli | 11 | species | invertebrates | helminths | 106947 |
| mathevotaenia symmetrica | -3 | species | | helminths | 1573891 |
| mayaro virus | 11 | species | viruses | viruses | 59301 |
| measles virus | 119 | species | viruses | viruses | 11234 |
| mecistocirrus digitatus | 5 | species | invertebrates | helminths | 237660 |
| medicopsis romeroi | 4 | species | plants | fungi | 1234271 |
| megamonas hypermegale | 5 | species | bacteria | bacteria | 158847 |
| megasphaera | 44 | genus | bacteria | | 906 |
| menangle virus | 12 | species | viruses | viruses | 152219 |
| meningonema peruzii | 1 | species | | helminths | |
| mesocestoides lineatus | 12 | species | invertebrates | helminths | 160008 |
| mesocestoides variabilis | 2 | species | | helminths | |
| metagonimus minutus | -3 | species | | helminths | |
| metagonimus yokogawai | 6 | species | invertebrates | helminths | 84529 |
| metarhizium marquandii | 10 | species | plants | fungi | 64636 |
| metarhizium viride | 4 | species | plants | fungi | 858349 |
| metorchis conjunctus | 3 | species | | helminths | |
| meyerozyma guilliermondii | 42 | species | plants | fungi | 4929 |
| microascus cinereus | 5 | species | plants | fungi | 186339 |
| microascus cirrosus | 3 | species | plants | fungi | 5595 |
| microdochium nivale | 32 | species | plants | fungi | 5520 |
| microfilaria bolivarensis | 2 | species | | helminths | |
| micronema deletrix | 16 | species | plants | | |
| microsporum audouinii | 18 | species | plants | fungi | 34393 |
| microsporum equinum | 8 | species | plants | fungi | 74041 |
| microsporum ferrugineum | 8 | species | plants | fungi | 77205 |
| microsporum gallinae | 4 | species | plants | fungi | 69892 |
| microsporum gypseum | 32 | no rank | plants | fungi | 489714 |
| microsporum persicolor | 5 | species | plants | fungi | 190483 |
| microsporum praecox | 2 | species | plants | fungi | 328624 |
| microsporum vanbreuseghemii | 1 | species | plants | fungi | 328623 |
| mogibacterium timidum | 11 | species | bacteria | bacteria | 35519 |
| mokola virus | 26 | species | viruses | viruses | 12538 |
| molluscum contagiosum virus | 36 | species | viruses | viruses | 10279 |
| moniezia expansa | 31 | species | invertebrates | helminths | 28841 |
| moniliella suaveolens | 3 | species | plants | fungi | 64615 |
| moniliformis moniliformis | 14 | species | invertebrates | helminths | 10237 |
| monkeypox virus | 35 | species | viruses | viruses | 10244 |
| monongahela virus | 3 | no rank | | viruses | 2259728 |
| moraxella atlantae | 5 | species | bacteria | bacteria | 34059 |
| moraxella bovis | 35 | species | bacteria | bacteria | 476 |
| moraxella catarrhalis | 87 | species | bacteria | bacteria | 480 |
| moraxella caviae | 6 | species | bacteria | bacteria | 34060 |
| moraxella cuniculi | 4 | species | bacteria | bacteria | 34061 |
| moraxella lacunata | 14 | species | bacteria | bacteria | 477 |
| moraxella lincolnii | 1 | species | bacteria | bacteria | 90241 |
| moraxella liquefaciens | 2 | species | | bacteria | |
| moraxella nonliquefaciens | 16 | species | bacteria | bacteria | 478 |
| moraxella osloensis | 16 | species | bacteria | bacteria | 34062 |
| moraxella ovis | 11 | species | bacteria | bacteria | 29433 |
| morganella morganii | 46 | species | bacteria | bacteria | 582 |
| mucambo virus | 7 | species | viruses | viruses | 60875 |
| mucor circinelloides | 27 | species | plants | fungi | 36080 |
| mucor hiemalis | 29 | species | plants | fungi | 64493 |
| mucor indicus | 8 | species | plants | fungi | 64623 |
| mucor racemosus | 26 | species | plants | fungi | 4841 |
| mucor ramosissimus | 5 | species | plants | fungi | 90264 |
| multiceps brauni | -3 | species | | helminths | |
| multiceps glomeratus | -3 | species | | helminths | |
| multiceps longihamatus | 1 | species | | helminths | |
| multiceps serialis | 4 | species | | helminths | |
| mumps virus | 61 | species | viruses | viruses | 11161 |
| murray valley encephalitis virus | 28 | species | viruses | viruses | 11079 |
| myceliophthora thermophila | 26 | species | plants | fungi | 573728 |
| mycobacterium abscessus | 38 | species | bacteria | bacteria | 36809 |
| mycobacterium africanum | 28 | species | bacteria | bacteria | 33894 |