Lactococcus garvieae is one of the main causative agents of streptococcusis/lactococcosis in farmed fish particularly in rainbow trout causing remarkable losses each year. Genotyping of 20 isolates of Lactococcus garvieae strains recovered from the mortality of farmed rainbow trout in different provinces of Iran was performed using RAPD-PCR method. The gram-positive cocci were first obtained from the kidney tissues of diseased trout. The bacterial isolates were grown on brain heart agar (BHI) and were then identified by a specific PCR method. The recovered gram-positive cocci strains were identified as L. garvieae by producing a 1100bp PCR product Then bacterial genotyping were processed with RAPD-PCR using two distinct random primers: P5 and M13. The RAPD-PCR results showed that primer P5 was able to produce maximum of 3 bands and 4 banding patterns, but primer M13 produced maximum of 7 bands and 5 banding patterns. Accordingly, the phylogenetic tree of the RAPD-PCR product using UPMGA software and using the primer P5 included these strains in 2 major clusters and 4 genetic groups, but using the primer M13 included these strains into 2 major clusters and 5 genetic groups. The results of this study indicate that although there are some phenotypic similarities between isolates of L. garvieae in different regions of Iran, these isolates have noticeable genetic differences. Further studies are need to clarify whether such genetic diversity of the isolates are important for bacterial severity and prophylactic vaccination.