Inbred lines of fish have been widely exploited as model organisms to determine the effect of inbreeding, which is often closely related to fitness such as endurance and productivity compared to morphological traits. Until now, much is unknown about the effects of inbreeding to fish. In the present study, inbred lines of guppies were used to examine the inbreeding effect on morphological traits corresponding to genotype variation. Two strains, called AY and NA1, were selected from the closed culture system. Both strains showed different levels of inbreeding coefficients when compared to microsatellite markers. The AY strain was less inbred as compared to NA1 strain. However, correlation between the standard lengths with multilocus heterozygosity (MLH) at the individual level was observed in the AY, but not in the NA1 strain. This indicated that highly inbred animals have higher similarity in morphological traits as compared to less inbred ones. The inbreeding process showed the importance of heterozygosity, even in laboratory-reared animals. This experiment illustrated the effects of inbreeding towards morphological and genetic changes. ?