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<p>Abstract</p> <p>Background</p> <p>A major concern in malaria vaccine development is the polymorphism observed among different <it>Plasmodium </it>isolates in different geographical areas across the globe. The merozoite surface protein 1 (MSP-1) is a leading vaccine candidate antigen against asexual blood stages of malaria parasite. To date, little is known about the extent of sequence variation in the <it>Plasmodium vivax </it>MSP-1 gene (<it>Pvmsp-1</it>) among Indian isolates. Since <it>P. vivax </it>accounts for >50% of malaria cases in India and in Colombia, it is essential to know the <it>Pvmsp-1 </it>gene variability in these two countries to sustain it as a vaccine candidate. The extent of polymorphism in <it>Pvmsp-1 </it>gene among Indian and Colombian isolates is described.</p> <p>Methods</p> <p>The sequence variation in the region encompassing the inter-species conserved blocks (ICBs) five and six of <it>Pvmsp-1 </it>gene was examined. PCR was carried out to amplify the polymorphic region of <it>Pvmsp-1 </it>and the PCR products from twenty (nine Indian and 11 Colombian) isolates were sequenced and aligned with Belem and Salvador-1 sequences.</p> <p>Results</p> <p>Results revealed three distinct types of sequences among these isolates, namely, Salvador-like, Belem-like and a third type sequence which was generated due to interallelic recombination between Salvador-like sequences and Belem-like sequences. Existence of the third type in majority (44%) showed that allelic recombinations play an important role in PvMSP1 diversity in natural parasite population. Micro-heterogeneity was also seen in a few of these isolates due to nucleotide substitutions, insertions as well as deletions.</p> <p>Conclusions</p> <p>Intergenic recombination in the <it>Pvmsp-1 </it>gene was found and suggest that this is the main cause for genetic diversity of the <it>Pvmsp-1 </it>gene.</p>