The current distribution and abundance of the 40 species of Goodeidae fishes known from Mexico are described, and a total of 84 Evolutionarily Significant Units (ESUs) is designated within these species. Two species and four ESUs are likely extinct with no captive populations, and three species and eight ESUs are probably extinct in the wild but have at least one captive population in Mexico, the United States, or Europe. Of the 35 extant species, the analyses indicate that nine should be considered as critically endangered, 14 as endangered, nine as vulnerable, and only three as least concern. Twenty-seven of these species have experienced substantial declines in distribution or abundance or both since 2000, and only eight appear to have remained relatively stable. Of the 72 extant ESUs, our analyses indicate that 29 should be considered as critically endangered, 21 as endangered, 18 as vulnerable, and only four as least concern. Brief summaries of the historic and current distributions and abundance of each species are provided, as well as ESU. Three strategies are recommended to conserve Mexican goodeids: protect the best-quality remaining habitats where goodeids still persist, restore degraded habitat and re-introduce species or ESUs where practical, and establish captive populations to ensure continued survival of the many species and ESUs that will almost inevitably go extinct in the coming years. Limited resources require cooperation and collaboration between scientists, conservationists, and aquarium hobbyists for successful captive maintenance.

The subfamily Goodeinae is a group of fishes endemic to the Mexican highlands. Most of the species are restricted to small and isolated streams or springs. Within this subfamily, the genus Characodon is the earliest diverging lineage of which three species have been described: C. lateralis, C. audax, and C. garmani, with the latter, considered extinct. Characodon lateralis and C. audax are classed as endangered, and have been the subject of taxonomic controversy since their description: previous studies have recognized a genetic differentiation in two groups separated by the El Salto waterfall, but morphological analyses contradict these genetic results. We perform a phylogeographic study using the mitochondrial cytb gene and d-loop region to elucidate the evolutionary history of C. lateralis and C. audax. The results with both markers show the presence of two highly differentiated haplogroups; one distributed north and the other distributed south of the waterfall, with genetic distances of 1.7 and 13.1% with cytb and d-loop respectively, and divergence calculated to have occurred 1.41 Mya. Significant genetic structure was found within each haplogroup and suggests the existence of at least four Evolutionary Significant Units (ESUs) within the examined populations. The possible processes identified as contributing to the formation of differentiated genetic groups are isolation, low population size, recurrent bottlenecks, and the strong sexual selection exhibited by the genus.