México is the southernmost country in North America, and extends into Central America, south of the Isthmus of Tehuantepec. The northern half of México is located on the Temperate belt and is arid in character (Nearctic), while the rest is within the Tropical belt (Neotropical). Climate varies from extremely temperate desert in the north, to tropical humid in the south. México has more than 500 freshwater fish species, about 271 of them country endemics, and approximately 48 endemics from binational basins. There are still some 30–40 fish species not yet described. There are 563 fish species colonizing coastal flood plain species. In addition to the numbers of colonizing fishes, the burden of introduced exotics has also been growing. In 1904, only 4 species were recognized as exotics; by 1997 the number had increased to 94, and by 2008 to 115. The main fish collections in Mexico are at IPN, UNAM, and UANL and are the most representative, being national in scope, although concentrated in the tropics, central region, and general in coverage, respectively. The decline of the native fish fauna has been in focus in recent years, usually as trend-in-time comparisons, where the loss of native forms and increase of exotics and/or colonizer species is evident in many basins, mainly in Río Balsas, Río Grande, and Río Lerma-Santiago. As a result, the numbers of species reported at some degree of risk have been increasing also, from 17 in 1963 to 192 in 2005. The trends in colonizers, exotics, and species at risk among Mexican fishes are parallel. The Index of Biological Integrity (IBI), in either its geographical, or historical form (IBIh), has been applied to the Rio Grande/Río Bravo basin, USA and México. IBIh values go between 0–91 (average 31). Alien species are regarded as detrimental. Overall, the IBI trends have been similar in all regions, starting from 70–95% in upper reaches, decreasing to less than 0–35% in the lower reaches of West central basins, and then down to 15% or less near the Lower Rio Grande delta. Several alien species of plecos have been recognized in the rivers Balsas, Grijalva-Río Usumacinta complex, and, also, one in the Rio Grande. Mexican rivers are notoriously dewatered in the northern half of the country. Until 1962, the Rio Grande had an average runoff of 12,000+ millions of cubic meters/year; however by 2002 it was less than 2% of that value. The river went nearly dry along the Big Bend region and was dry for months in the delta region, both in 2002 and 2004. The Rio Grande is mostly dry north of the Río Conchos junction, its main Mexican tributary, and other tributaries provide now between 1% (Río San Juan) and 20% (Río Conchos) of pre-1960 runoff. A modified Index of Biological Integrity for Rio Grande resulted in grades from 70 to 95% of the baseline in upper reaches, less than 35% in lower reaches, to less than 15% near the coast. The Texan version of the IBI was not representative as it suppresses data on euryhaline fishes. The reports of total toxics were masked, since the sum should have included both organics and heavy metals exceeding USA regulations to the total count, but only one of the two was included.

This is the third compilation of imperiled (i.e., endangered, threatened, vulnerable) plus extinct freshwater and diadromous fishes of North America prepared by the American Fisheries Society's Endangered Species Committee. Since the last revision in 1989, imperilment of inland fishes has increased substantially. This list includes 700 extant taxa representing 133 genera and 36 families, a 92% increase over the 364 listed in 1989. The increase reflects the addition of distinct populations, previously non-imperiled fishes, and recently described or discovered taxa. Approximately 39% of described fish species of the continent are imperiled. There are 230 vulnerable, 190 threatened, and 280 endangered extant taxa, and 61 taxa presumed extinct or extirpated from nature. Of those that were imperiled in 1989, most (89%) are the same or worse in conservation status; only 6% have improved in status, and 5% were delisted for various reasons. Habitat degradation and nonindigenous species are the main threats to at-risk fishes, many of which are restricted to small ranges. Documenting the diversity and status of rare fishes is a critical step in identifying and implementing appropriate actions necessary for their protection and management.

The variation and composition of Mexican wild trout mitochondrial DNA haplotypes throughout northwestern Mexico was determined by means of polymerase chain reaction-restriction fragment polymorphism analysis (PCR-RFLP), of one region of mitochondrial DNA between cytochrome b and the D-loop. This analysis was based on 261 specimens taken in 12 basins and four hatcheries from northwestern Mexico. From 23 haplotypes, 15 wild trout haplotypes were identified and classified in four groups: (1) one restricted to Nelson's trout (Oncorhynchus mykiss nelsoni), (2) four restricted to R¡o Mayo and R¡oYaqui trout (O. mykiss sspp.), (3) six to Mexican golden trout (O. chrysogaster) with two subgroups, and (4) one exclusive to R¡o Piaxtla trout. Distributions of native haplotypes broadly overlap the distribution of non-native hatchery rainbow trout reflecting the historical management of introductions of exotic rainbow trout and the artificial transference of these trout among basins.

We examined foraging behavior (microhabitat use and feeding behavior) in a trophically polymorphic cichlid fish, Herichthys minckleyi, to address several questions regarding resource partitioning in this threatened species. These include: (1) do morphotypes demonstrate different foraging behaviors? (2) do individuals within a morphotype vary in their foraging behavior (e.g. are some individuals specialists, only using a subset of available resources, while other are generalists)? (3) do foraging behaviors vary between isolated pools? (4) do foraging behaviors vary across seasons? We quantified microhabitat use and feeding behavior for over 100 individuals (of two morphotypes) feeding freely in two isolated pools (populations) and across two seasons (winter and summer). We found differences in foraging behavior between morphotypes and individual specializations within morphotypes; i.e. some individuals specialize on certain food resources by using a few feeding behaviors within a subset of microhabitats, whereas others employ a range feeding behaviors across many microhabitats. Foraging behavior also varied between pools and across seasons. This spatial and temporal variation in foraging behavior and resource use may serve to maintain this polymorphism, as the relative fitness of the each morph may vary over space and time

The evolutionary viability of an endangered species depends upon gene flow among subpopulations and the degree of habitat patch connectivity. Contrasting population connectivity over ecological and evolutionary timescales may provide novel insight into what maintains genetic diversity within threatened species. We employed this integrative approach to evaluating dispersal in the critically endangered Coahuilan box turtle (Terrapene coahuila) that inhabits isolated wetlands in the desert-spring ecosystem of Cuatro Ciénegas, Mexico. Recent wetland habitat loss has altered the spatial distribution and connectivity of habitat patches; and we therefore predicted that T. coahuila would exhibit limited movement relative to estimates of historic gene flow. To evaluate contemporary dispersal patterns, we employed mark-recapture techniques at both local (wetland complex) and regional (inter-complex) spatial scales. Gene flow estimates were obtained by surveying genetic variation at nine microsatellite loci in seven subpopulations located across the species' geographic range. The mark-recapture results at the local spatial scale reveal frequent movement among wetlands that was unaffected by inter-wetland distance. At the regional spatial scale, dispersal events were relatively less frequent between wetland complexes. The complementary analysis of population genetic substructure indicates strong historic gene flow (global FST = 0.01). However, a relationship of genetic isolation by distance across the geographic range suggests that dispersal limitation exists at the regional scale. Our approach of contrasting direct and indirect estimates of dispersal at multiple spatial scales in T. coahuila conveys a sustainable evolutionary trajectory of the species pending preservation of threatened wetland habitats and a range-wide network of corridors.