Crossbreeding for 3 groups (A, B, C) of Taiwanese red tilapia (Oreochromis sp.) was conducted. Results showed that progeny of group A were pure red or spotted, number of spots was variable, progeny of group B were pure red or spotted, number of spots was less than 10, and progeny of group C were pure red, white or blotched. On the mean standard length, total length and body weight, pure red and spotted progeny of group A and B were not significantly different (p>0.05), respectively; as for the group C, pure red and blotched progeny were not significantly different (p>0.05), while both were were significantly different (p<0.05) to white progeny.RAPD biotechnology could be used to identify between C05r and D08r strains, C06r and D08r strains, and D09r and D10r strains. The genetic variation of A10r, A16r, C02r, C05r and C06r were all low, analyzed by the D-loop of mitochondrial DNA, owing to the inbreeding.