For the management of endangered species, a periodic health assessment is important, as diet in captivity is restricted due to cost and some nutrients are lost during the processing, storage and thawing of fish. The objective of this study was to compare and assess the nutritional, as well as the physiological health of both the captive and free-ranging Yangtze Finless Porpoises (YFPs) through biochemical markers, selected electrolytes, enzymes and hematological parameters. Our results showed statistically significantly (P < 0.05) higher levels of some biochemical markers (HDL-c/LDL-c, globulin, TP, Urea, Creatinine and BUN), enzymes (GGT), electrolytes (K+, Na+, PO43- and Mg2+) and hematological (WBCs, lymphocytes, eosinophil) parameters in wild compared to the captive populations. However, the captive population also showed significantly (P < 0.05) higher levels of some biochemical markers (LDL-c, albumin and albumin/globulin), enzymes (AMS), electrolytes (Cl-) and complete blood count (neutrophil, monocytes and basophil) parameters versus wild populations. Differences in the parameters of captive YFPs could be due to their limited diet of only three fish species as well as their environment (captivity). Whereas, wild YFPs, continuously feed on a large variety of live fish species and shrimp as they travel long distances. Our results suggest that mineral supplements be added to their diet. As well, improved physical fitness training and hygienic conditions are required for the effective management of captive finless porpoises.