| Scientific name | Common name | Type of species | Level of threat |
|---|
| Macadamia tetraphylla | Rough-shelled Bush Nut | Plant > Trees | Vulnerable |
| Macronectes giganteus | Southern Giant-Petrel | Animal > Birds | Endangered |
| Macronectes halli | Northern Giant-Petrel | Animal > Birds | Vulnerable |
| Macropus dorsalis | Black-striped Wallaby | Animal > Marsupials | Endangered |
| Macropus parma | Parma Wallaby | Animal > Marsupials | Vulnerable |
| Macrozamia humilis | Inverell Cycad | Plant > Ferns and Cycads | Endangered |
| Macrozamia johnsonii | Johnson’s Cycad | Plant > Ferns and Cycads | Endangered |
| Maireana cheelii | Chariot Wheels | Plant > Herbs and Forbs | Vulnerable |
| Manorina melanotis | Black-eared Miner | Animal > Birds | Endangered |
| Maroota Sands Swamp Forest | Maroota Sands Swamp Forest | Community > Threatened Ecological Communities | Endangered Ecological Community |
| Marsdenia longiloba | Slender Marsdenia | Plant > Epiphytes and climbers | Endangered |
| Marsdenia viridiflora subsp. viridiflora - endangered population | Marsdenia viridiflora subsp. viridiflora in the Bankstown, Blacktown, Camden, Campbelltown, Fairfield, Holroyd, Liverpool and Penrith local government areas | Plant > Endangered Populations | Endangered Population |
| Mastacomys fuscus | Broad-toothed Rat | Animal > Rodents | Vulnerable |
| Mastacomys fuscus - endangered population | Broad-toothed Rat at Barrington Tops in the Gloucester, Scone and Dungog LGAs | Animal > Endangered Populations | Endangered Population |
| Maundia triglochinoides | Maundia triglochinoides | Plant > Herbs and Forbs | Vulnerable |
| McKies Stringybark/Blackbutt Open Forest in the Nandewar and New England Tableland Bioregions | McKies Stringybark/Blackbutt Open Forest | Community > Threatened Ecological Communities | Endangered Ecological Community |
| Megaptera novaeangliae | Humpback Whale | Animal > Marine Mammals | Vulnerable |
| Melaleuca armillaris Tall Shrubland in the Sydney Basin Bioregion | Melaleuca armillaris Tall Shrubland in the Sydney Basin Bioregion | Community > Threatened Ecological Communities | Endangered Ecological Community |
| Melaleuca biconvexa | Biconvex Paperbark | Plant > Trees | Vulnerable |
| Melaleuca deanei | Deane's Paperbark | Plant > Shrubs | Vulnerable |
| Melaleuca groveana | Grove's Paperbark | Plant > Shrubs | Vulnerable |
| Melaleuca irbyana | Weeping Paperbark | Plant > Trees | Endangered |
| Melaleuca sp. Megalong Valley | Megalong Valley Bottlebrush | Plant > Shrubs | Vulnerable |
| Melanodryas cucullata cucullata | Hooded Robin (south-eastern form) | Animal > Birds | Vulnerable |
| Melichrus hirsutus | Hairy Melichrus | Plant > Shrubs | Endangered |
| Melichrus sp. 'Gibberagee' | Narrow-leaf Melichrus | Plant > Shrubs | Endangered |
| Melicope vitiflora | Coast Euodia | Plant > Trees | Endangered |
| Melithreptus gularis gularis | Black-chinned Honeyeater (eastern subspecies) | Animal > Birds | Vulnerable |
| Menippus fugitivus - endangered population | Menippus fugitivus (a beetle) population in the Sutherland Shire | Animal > Endangered Populations | Endangered Population |
| Menura alberti | Albert's Lyrebird | Animal > Birds | Vulnerable |
| Meridolum corneovirens | Cumberland Land Snail | Animal > Invertebrates | Endangered |
| Micromyrtus blakelyi | Micromyrtus blakelyi | Plant > Shrubs | Vulnerable |
| Micromyrtus grandis | Severn River Heath-myrtle | Plant > Shrubs | Endangered |
| Micromyrtus minutiflora | Micromyrtus minutiflora | Plant > Shrubs | Endangered |
| Microstrobos fitzgeraldii | Dwarf Mountain Pine | Plant > Shrubs | Endangered |
| Microtis angusii | Angus's Onion Orchid | Plant > Orchids | Endangered |
| Milton Ulladulla Subtropical Rainforest in the Sydney Basin Bioregion | Milton Ulladulla Subtropical Rainforest in the Sydney Basin Bioregion | Community > Threatened Ecological Communities | Endangered Ecological Community |
| Miniopterus australis | Little Bentwing-bat | Animal > Bats | Vulnerable |
| Miniopterus schreibersii oceanensis | Eastern Bentwing-bat | Animal > Bats | Vulnerable |
| Mitrasacme pygmaea | Pygmy Bishop's Hat | Plant > Herbs and Forbs | Endangered |
| Mixophyes balbus | Stuttering Barrred Frog | Animal > Amphibians | Endangered |
| Mixophyes fleayi | Fleay's Barred Frog | Animal > Amphibians | Endangered |
| Mixophyes iteratus | Giant Barred Frog | Animal > Amphibians | Endangered |
| Moist Shale Woodland in the Sydney Basin Bioregion | Moist Shale Woodland in the Sydney Basin Bioregion | Community > Threatened Ecological Communities | Endangered Ecological Community |
| Monarcha leucotis | White-eared Monarch | Animal > Birds | Vulnerable |
| Monotaxis macrophylla | Large-leafed Monotaxis | Plant > Herbs and Forbs | Endangered |
| Monotoca rotundifolia | Trailing Monotoca | Plant > Shrubs | Endangered |
| Montane Peatlands and Swamps of the New England Tableland, NSW North Coast, Sydney Basin, South East Corner, South Eastern Highlands and Australian Alps | Montane Peatlands and Swamps | Community > Threatened Ecological Communities | Endangered Ecological Community |
| Mormopterus 'Species 6' | Hairy-nosed Freetail Bat | Animal > Bats | Endangered |
| Mormopterus beccarii | Beccari's Freetail-bat | Animal > Bats | Vulnerable |
| Mormopterus norfolkensis | Eastern Freetail-bat | Animal > Bats | Vulnerable |
| Mount Gibraltar Forest in the Sydney Basin Bioregion | Mount Gibraltar Forest in the Sydney Basin Bioregion | Community > Threatened Ecological Communities | Endangered Ecological Community |
| Mt Canobolas Xanthoparmelia Lichen Community | Mt Canobolas Xanthoparmelia Lichen Community | Community > Threatened Ecological Communities | Endangered Ecological Community |
| Muehlenbeckia costata | Scrambling Lignum | Plant > Epiphytes and climbers | Vulnerable |
| Muellerina myrtifolia | Myrtle-leaf Mistletoe | Plant > Epiphytes and climbers | Endangered |
| Myall Woodland in the Darling Riverine Plains, Brigalow Belt
South, Cobar Peneplain, Murray-Darling Depression, Riverina and NSW South western Slopes bioregions | Myall Woodland in the Darling Riverine Plains, Brigalow Belt
South, Cobar Peneplain, Murray-Darling Depression, Riverina and NSW South western Slopes bioregions | Community > Threatened Ecological Communities | Endangered Ecological Community |
| Myotis macropus (formally Myotis adversus) | Large-footed Myotis | Animal > Bats | Vulnerable |