The A07r, C03r and C07r strains of Taiwanese red tilapia (Oreochromis sp.) stocked at Freshwater Aquaculture Research Center were discriminated and their genetic variations were analyzed by using RAPD and PCR-RFLP. Besides, breeding of A07r x A07r, C03r x C03r and C03r x C07r was carried out to obtain the pure red strain.In regard of RAPD analysis, C03r strain could be distinguished from C07r strain by using OPA 07 random primer, and C07r strain could be distinguished from A07r strain by using OPA 15 random primer. In the use of PCR-RFLP analysis on the mtDNA D-loop region, C03r strain could be distinguished from A07r and C07r strains. Haplotype diversity of the mtDNA D-Loop region in A07r, C03r and C07r strains was 0, demonstrating a very low genetic variation within the strain.In breeding, all fry were white. Their color changed as they grew up. After five-month growing period, the crosses of A07r × A07r yielded two types of progeny-pure red and blotched red patterns, but their mean body weight and body length were not significantly different (p > 0.05). There was a similar result in the crosses of C03r × C03r. However, the crosses of C03r × C07r yielded three types of progeny as pure red, blotched red and white ones. The mean body weight and body length between pure red and blotched red types was not significantly different (p > 0.05), while white-type progeny had lower mean body weight and body length as compared to pure red and blotched red types (p < 0.05). Since the growth of pure and blotched red progeny was not significantly different within each breeding group, and the blotched red type had only a few blotches, it was speculated that there was little difference of genetic factors between these two types.