The mechanisms by which Potato virus Y variants are generated and selected are still unclear. Spontaneous mutations generated by uncorrected replication error and recombination events between viral isolates during co-infection of plant cells are the main likely source of genetic diversity. This high level of diversity generation is essential for virus evolution and survival in different environments. Different PVY strain groups have appeared over time: firstly, non-recombinant PVYC, PVYO and PVYN strains and, more recently, recombinant PVYN-Wi and PVYNTN strains with novel biological characteristics and the ability to cause potato tuber necrotic ringspot disease (PTNRD). Increased fitness of the recombinant strains appears to have enabled them to replace the non-recombinant variants in most potato growing areas of the world. Partial sequencing of PVY genome (P1, HC-Pro, CP, recombinant junctions) and whole genome sequencing has shown that non-recombinant and recombinant variants are present in potatoes and other plant hosts. Phylogenetic analyses have been applied to document changes in viral isolates and to establish the relationships between different viral isolates. Traditional phylogenetic analysis was, however, developed for bifurcating phylogenies and not for analysing recombination, as a result of which this presents challenges to these analyses which will be outlined in this chapter. The ongoing worldwide studies on PVY characterisation suggest that new variants with distinct biological properties are likely to be uncovered in the future. Emerging technologies such as next generation sequencing will provide valuable insights into PVY population dynamics and evolution in future.