Thirty five monoconidial isolates of the fungal culture collection Pyricularia grisea were examined, to identify the vegetative compatibility groups and characterize the genetic diversity of isolates as through rep-PCR genomic fingerprinting. The isolates were collected from ricefields during 1997-1999. Genetic diversity of P. grisea isolates was studied as based on DNA fingerprinting through rep-PCR using two primers previously designed based on the nucleotidal sequence in ERIC and BOX regions. They generated variable length fragments ranging from 400 to 2500 bp. Phenetic analysis let to differentiation of four distinct clonal lineages designated as A to D. Clonal lineage A with 74.28% frequency, constituted the largest fingerprinting group. For VCG analyses nit mutants were obtained from fast growing sectors on Minimal Medium (MM) containing 5% potassium chlorate. Complementation between nit mutants of isolates was tested on MM. Four vegetative compatibility groups were determined including VCG1, VCG2, VCG3 and VCG4. Group VCG3 comprised of 14 isolates was the dominant VC group among others. This study revealed that isolates obtained from rice were designated in the four VC groups forming heterokaryon with each other; however these isolates were separated with more than 80% similarity from each other using rep-PCR marker with most of isolates being VCG3 were determined in A clonal lineage. Both VCGs and rep-PCR analyses determined low genetic diversity in P. grisea population from rice.