The Owens Tui Chub Siphateles bicolor snyderi has become endangered by introgressive hybridization with the Lahontan Tui Chub S. bicolor obesa since the 1960s. Adequate conservation strategies require prior identification of pure populations, which is usually difficult because the diagnostic features presented in the formal subspecies description do not always allow unequivocal determination of populations. In the present study, the shape and some meristic features of the scales, along with the shape of other bones with taxonomic value, were analyzed to distinguish both parental subspecies and their hybrids in samples diagnosed in a previous work using microsatellite DNA. Scales, pharyngeal arches, dentaries, cleithra, and opercula of 211 individuals from 16 localities across the Owens River and neighbouring basins in California and Nevada were compared. The results show that the meristic parameters of the scales were in agreement with values provided by Miller (1973) for the parental subspecies. Shape analyses were based on landmark or Fourier methods, depending on the shape characteristic of each structure. Geometric morphometric analyses provided variable discriminatory power between subspecies depending on the studied bone. In scales, pharyngeal arches, and dentaries, the derived morphological patterns matched the shape descriptions set forth by Miller (1973) for both parental subspecies. In all cases, the observed morphometric variability of hybrids was too high to separate them from parental subspecies. However, joint analysis of the five structures produced groupings that were concordant with the genetic analyses: localities of parental subspecies in separate groups and an intermediate group with the hybrid swarm localities that was morphologically closer to Lahontan. Finally, a new derived parameter (the ratio between scale lengths from the anterior and posterior body) is suggested as a promising tool for rapid discrimination of Owens Tui Chub from Lahontan Tui Chub and their hybrid populations.