Complementarity analysis is a tool that attempts to maximize marginal increase in biodiversity conservation at the lowest cost. It has been used as a reserve selection criterion to maximize among-reserve diversity with minimal reserve number. Although genetic diversity is a significant component of biodiversity as a whole, species diversity has been used exclusively for complementarity-based reserve selection because of the relative ease of obtaining species richness data relative to genetic data. We compared concordance between complementarity indices calculated from allelic richness and species richness among pairs of springs in the northern Chihuahuan Desert, using published endemic amphipod (Gammarus spp.) and Gambusia nobilis allozyme data and fish and benthic macroinvertebrate species lists. We then tested concordance between the pairs of complementarity indices using Mantel tests. Our results reveal high concordance among pairs of taxa and faunal communities, implying that complementarity-based reserve design in this ecosystem will be effective in conserving genetic biodiversity, even if selection is solely based on species richness and vice versa. We suggest further testing of concordance between genes and species in other ecosystems using multiple taxa and communities.