Original description as Cyprinodon macularius eremus:
- Miller, Robert Rush & L.A. Fuiman. 1987. "Description and conservation status of Cyprinodon macularius eremus, a new subspecies of pupfish from Organ Pipe Cactus National Monument, Arizona". Copeia. 1987(3):593-609 (ffm00177)
Conservation: Cyprinodon eremus is evaluated by the international union for the conservation of nature in the iucn red list of threatened species as (EN) endangered (2018). Cyprinodon eremus range of occurrence is believed to be less than 11 km2 in its native range. It occurs in just a few locations that are subject to ongoing declines resulting from habitat loss, degradation, water abstraction, pollutants, non-native species, and other unknown factors. C. eremus has faced past, and possibly ongoing, fluctuations in population size caused by unknown influences. This species is relatively intolerant of competition and predation, and it is easily displaced by introduced fishes. Cyprinodon eremus coexists with Gambusia affinis and Ameiurus melas in the Rio Sonoyta. G. affinis are increasing perhaps at the expense of C. eremus; the impact of the A. melas is uncertain but they are probably a predator (NatureServe et al., 2019).