Plasmodim vivax malaria accounts for more than 90% of malaria cases in Sri Lanka. There is limited information on the genetic heterogeneity of P. vivax in endemic areas of the country. Here we have assessed the potential of two P. vivax genes as genetic markers for their use in genotyping parasites collected from the field. DNA extracted from Geimsa-stained P. vivax positive slides were genotyped at two polymorphic loci: the P. vivax merozoite surface protein 3- alpha (Pvmsp-3alpha) and circumsporozoite protein (Pvcs). Analysis of these two genetic markers revealed 11 distinguishable variant types from the two genetic markers: 4 for Pvcs and 7 for Pvmsp-3alpha. The results indicate that the P. vivax parasite population is highly diverse in Sri Lanka, despite the low level of transmission.