Gobiocypris rarus Ye et Fu (1983) is an endemic cyprinid fish in China, and is considered to be an endangered species. From a conservation perspective, its population structure is interesting. In the present study, morphological variation, including morphometric and meristic traits, was assessed among wild samples collected in the upper Yangtze River basin. There were no significant meristic differences between sexes or among populations, except for scales in lateral line (LS). However, there were significant morphometric differences not only between sexes but also among populations. In discriminant function analysis, the first four discriminant functions explained 75.5% and 78% of the among-population morphometric variation for males and females, respectively. Almost all the truss network morphometric traits significantly contributed to population discrimination. By using all of the truss network morphometric traits, overall random assignments of male and female individuals into their original population were both 73.5%. In addition, the degree of differentiation in phenotypic traits (P_ST) significantly exceeds that in neutral molecular markers (F_ST). However, no significant correlation between P_ST and F_ST was found in males or females. Overall, these results suggest that two evolutionary processes, including phenotypic plasticity and natural selection, may contribute to the morphological patterns observed in G. rarus.