In this study, we examined the population structure and genetic diversity of Citrus psorosis virus (CPsV) in Morocco. Analysis of the coat protein partial sequences of 34 isolates collected in the three main citrus-growing areas of Morocco showed that CPsV grouped in three major groups, with low within-group nucleotide diversity. Analyses indicated that CPsV genetic diversity is not structured by the geographic origin of the CPsV isolates. The genetic variation resulting from mutations depends on evolutionary forces that have contributed to the shaping of the genetic structure and diversity of the CPsV populations analyzed here: negative selective pressure for amino acid variation, recombination between variants or mixed infection, genetic drift induced by the founder effect associated with the transmission process, and migration explained by the exchange of infected propagative plant material.