Captive breeding is an effective strategy for the conservation of endangered species, but it may affect their phenotypes in many cases. To investigate how captive breeding influences morphology and health status of Shinisaurus crocodilurus, we compared the morphological traits and bacterial infection rate for both new hatched ones and sub-adults of Shinisaurus crocodilurus born in captive breeding population and in the wild population. We got the following results: (1) the body size of new born ones was not showed a significant difference between both groups, but the sub-adults born in captive population was larger than those born in wild population by Bonferroni post hoc test (Fig. 1). (2) The tail autotomy rate was significantly lower for those born in captive population at both age stages (Fisher′s exact test, all P < 0.05; Fig. 2a). (3) The Bacterial infection rate was highest in sub-adults born in captive breeding population, but no significant difference was found between the two groups (Fisher′s exact test, all P > 0.05; Fig. 2b). Our study indicates captive breeding has enhanced growth rate, reduced predation risk. However, there is a slightly potential to increase the bacterial infection rate. More cautions should be taken in disease controlling in captive breeding programs for S. crocodilurus.