Aphis gossypii Glover is cosmopolitan pest aphid, known to be represented by host-associated lineages. Although it is widespread in the Pacific Basin, there has been no assessment of this species in this region. We examined patterns of morphological variation within and among populations collected across hosts and islands using multivariate morphometric analyses. Genetic variation was determined using microsatellite flanking region sequences and mitochondrial cytochrome oxidase subunit 1. This study confirmed the existence of genetically distinct host-associated lineages. We found that host plant affects morphological expression and therefore morphological criteria cannot be used to identify lineages. Comments are provided on the origin and maintenance of these host lineages and implications for management of this important pest aphid species.