[3][5] While most Cyprinodon species have separate distributions, seven (C. beltrani, C. esconditus, C. labiosus, C. maya, C. simus, C. suavium and C. verecundus) are endemic in Lake Chichancanab in Quintana Roo, Mexico,[6][7] and three (the endemic C. brontotheroides and C. desquamator, and the widespread C. variegatus) live in the hypersaline lakes on San Salvador Island in the Bahamas.

[2] Although the individual Cyprinodon species often have a highly specific habitat, overall the genus occurs in a remarkable range of places, such as springs (including those isolated in deserts), pools, lakes, coastal lagoons, creeks, streams and rivers.

C. arcuatus, C. ceciliae, C. inmemoriam, C. nevadensis calidae and an undescribed species popularly known as the "Perrito de Sandia" are already extinct.

[18][20][21] A few other Mexican species still considered endangered or vulnerable by the IUCN, including at least C. maya, C. simus and C. verecundus of Lake Chichancanab, also appear to only survive in captivity.

[19] Among the species that survive in the wild, the rarest is perhaps C. diabolis from the tiny Devils Hole in Nevada; in recent decades its population has fluctuated between a few tens and a few hundred individuals.

[24] Primary threats to pupfish are habitat loss due to water extraction, drought and pollution, and introduced species.

[3][19] Most Cyprinodon species feed on algae, cyanobacteria and detritus, but may also supplement their diet with small crustaceans and aquatic insect larvae.

[25] Especially those from habitats that experience major environmental fluctuations (for example, large variations in temperature) rapidly reach maturity and are already able to breed when 1–1.5 month old.