Swimming performance is an important capacity for fish species because it is closely related to the ability to gain food, to predator avoidance and to other daily activities. As an important locomotive organ for most fish species, the caudal fin plays a crucial role in propelling and guiding fish during swimming and thus the shape, size and stiffness of the caudal fin are all expected to strongly affect swimming performance. In nature, the caudal fins of fish species are frequently lost to some extent by aggressive behaviour, predation and diseases. To investigate the effects of caudal fin loss and regeneration on fast-start performance of crucian carp (Carassius auratus, inhabiting in still water) and pale chub (Zacco platypus, inhabiting in rip current), 16 juveniles of both crucian carp (body length, (6.27 ± 0.04) cm) and pale chub (body length, (6.14 ± 0.12) cm) were allocated to two groups, respectively. One group (8 fish for each treatment) for the treatment of caudal-fin-amputation-regeneration (20 days) and re-amputation, the other group (8 fish for each treatment) for control. The movement of each fish was recorded by a high-speed camera after an electric stimulation for the analysis of fast-start parameter. Furthermore, the morphological parameters such as body length (L), body height (H), fitness ratio (FR), caudal fin aspect ratio (AR), relative caudal fin area ratio and caudal fin index (FI) in the two cyprinid fish species were measured. The experimental water temperature was maintained at (25.0 ± 0.5)℃. The results showed that the crucian carp showed a significant lower FR and higher FI than pale chub (P < 0.01), but the maximum linear velocity (V_max), escape distance (d), relative turning radius (TRr) and bending coefficient (BC) showed no significant difference between the two cyprinid fish species. The V_max, d and TRr during fast-start process of both fish species decreased significantly after caudal fin loss (P < 0.01), with the V_max of crucian carp decreased by 39% while that of pale chub decreased by 24% after caudal fin loss. After 20 days' recovery, the areas of caudal fin of both fish species recovered about 60% those of the caudal-fin-intact fish. However, the V_max, d, RTr and BC of both caudal-fin-regenerated crucian carp and pale chub showed no significant difference compared with those of the control groups, respectively. Compared to the caudal-fin-intact fish, the decrease of V_max of crucian carp and pale chub after the second amputation (17% and 9%) was smaller than the first amputation (39% and 24%). The decrease ratio between the first and the second caudal fin amputation in crucian carp was larger than that of pale chub. However, the bending coefficient (BC) of pale chub increased significantly after the second caudal fin amputation compared with those of fin-intact group (P = 0.046). The results indicated that (1) the caudal fin of crucian carp played a more important role than that of pale chub during fast-start movement; and (2) the pale chub which prefer to rip current habitat showed more significant functional compensation after 20 days' recovery.