Potato yellow vein virus (PYVV) is currently one of the most important viruses that infects potatoes in Colombia and other Andean countries, causing losses in the production of tubers ranging from 25% to 50%. This study analyzed the genetic variability of different viral isolates collected in the department of Nariño, Colombia, through bioinformatics analysis of the sequences of three genes encoding the capsid protein (CP), the heat-shock protein 70 (Hsp70) and the minor capsid protein (CPm). We found that CPm is the gene that shows greater diversity, with higher values of nucleotide substitution and evidence of recombination. Based on an analysis of the haplotype map using nucleotide sequences of the CPm, we propose a model of putative recombination in this genomic region. The non-recombinant segments are supported by the results of the program GARD (Genetic Algorithm for Recombination Detection), phylogenetic trees and the paired values of genetic distances of each non-recombinant segments. The model clearly shows that the amino region of the CPm is prone to recombination. To our knowledge, this is the first report of genetic recombination as an evolutionary strategy in the CPm of PYVV.