The genus Rhoadsia is endemic to western Ecuador and northern Peru and includes two described species that differ in body form, size, and the elevations at which they occur. Unfortunately, there is uncertainty about the number of species that should be recognized in the genus and the causes of the morphological variation documented within and between species. We take advantage of a survey of the fish fauna of the Santa Rosa River in southwestern Ecuador that yielded large numbers of Rhoadsia altipinna, to expand knowledge of the ecological, morphological, and genetic variation of this species. Specimens were collected at five sites at elevations between 31 and 613 m above sea level, and each site was sampled in December 2012 and July 2013. Rhoadsia altipinna was the second most abundant species in the Santa Rosa River, was one of only three species collected at all elevations, and was more common in pool mesohabitats than riffle mesohabitats. Geometric morphometric analysis of body shape variation indicated strong sexual dimorphism and allometry, with body depth increasing substantially with size. More interestingly, body depth declined with elevation in the Santa Rosa River. This intraspecific pattern of variation mirrored the interspecific divergence reported between the two recognized species. Lower elevation R. altipinna are known to be deeper bodied than high elevation R. minor. However, specimens of R. minor from the paratype series measured for comparison were still more streamlined than all Santa Rosa R. altipinna examined, including those collected at the highest elevations and juveniles. Although body shape differed significantly between Santa Rosa River R. altipinna and other populations from southwestern Ecuador, the geographic differences appeared small relative to variation attributable to sexual dimorphism and allometry. Finally, sequencing of a fragment of the cytochrome oxidase I gene for samples from the Santa Rosa River and two samples from the neighboring Guayas River drainage failed to recover a monophyletic Santa Rosa lineage. Although haplotype frequencies differed significantly between the Santa Rosa and Guayas River samples, the lack of monophyly and similarity among the haplotypes make the genetic data more consistent with divergence of geographically isolated populations within a single species than with interspecific divergence. Further analysis of morphological and genetic variation throughout the range of the genus will help elucidate its ecological and evolutionary dynamics.