The intraspecific variations in the morphology of populations of cotton mealybug Phenacoccus solenopsis Tinsley (Pseudococcidae: Hemiptera) from cotton, okra and hibiscus were analyzed. The principal component analysis and discriminant functional analysis revealed a wide range of morphological variations in the critical taxonomic characters among the populations. Genetic diversity in the populations using mitochondrial cytochrome oxidase 1 (mtCO-1) sequences revealed that there were no significant variations of P. solenopsis collected from various hosts in Asia. However, the phylogenetic tree with available sequences in the NCBI GenBank of different geographic regions revealed a distinct separation between Asian and American populations. Thus, this study adds to our knowledge of the host-associated morphological variations and genetic diversity of P. solenopsis populations.