Species described (32):
- Allodontichthys hubbsi Miller & Uyeno, 1980 (Allodontichthys), valid
- Ameca splendens Miller & Fitzsimons, 1971 (Ameca), valid
- Cualac tessellatus Miller, 1956 (Cualac), valid
- Cyprinodon alvarezi Miller, 1976 (Cyprinodon), valid
- Cyprinodon atrorus Miller, 1968 (Cyprinodon), valid
- Cyprinodon bifasciatus Miller, 1968 (Cyprinodon), valid
- Cyprinodon macularius eremus Miller & Fuiman, 1987 (Cyprinodon), valid
- Cyprinodon macrolepis Miller, 1976 (Cyprinodon), valid
- Cyprinodon meeki Miller, 1976 (Cyprinodon), valid
- Cyprinodon nazas Miller, 1976 (Cyprinodon), valid
- Cyprinodon pisteri Miller & Minckley, 2002 (Cyprinodon), valid
- Dactyloscopus amnis Miller & Briggs, 1962 (Dactyloscopus), valid
- Fundulus persimilis Miller, 1955 (Fundulus), valid
- Gambusia aurata Miller & Minckley, 1970 (Gambusia), valid
- Gambusia eurystoma Miller, 1975 (Gambusia), valid
- Gila ditaenia Miller, 1945 (Gila), valid
- Hyporhamphus patris Miller, 1945, synonym
- Cichlasoma regani Miller, 1974 (Maskaheros), valid
- Megupsilon aporus Miller & Walters, 1972 (Megupsilon), valid
- Rivulus robustus Miller & Hubbs, 1974 (Millerichthys), valid
- Poecilia catemaconis Miller, 1975 (Poecilia), valid
- Poecilia chica Miller, 1975 (Poecilia), valid
- Poeciliopsis catemaco Miller, 1965 (Poeciliopsis), valid
- Poeciliopsis lucida Miller, 1960 (Poeciliopsis), valid
- Poeciliopsis monacha Miller, 1960 (Poeciliopsis), valid
- Poeciliopsis prolifica Miller, 1960 (Poeciliopsis), valid
- Poeciliopsis turneri Miller, 1975 (Poeciliopsis), valid
- Poeciliopsis viriosa Miller, 1960 (Poeciliopsis), valid
- Profundulus hildebrandi Miller, 1950 (Profundulus), valid
- Rhamdia reddelli Miller, 1984 (Rhamdia), valid
- Cichlasoma socolofi Miller & Taylor, 1984 (Thorichthys), valid
- Xiphophorus gordoni Miller & Minckley, 1963 (Xiphophorus), valid
Genera described (3):
- Ameca Miller & Fitzsimons, 1971, valid
- Cualac Miller, 1956, valid
- Megupsilon Miller & Walters, 1972, valid