Phylogenetic relationships amongst Megastigmus species (Chalcidoidea:Torymidae) associated with conifer seeds were inferred from DNA sequence data.Twenty-nine species of seed chalcids were analysed using two different genes,cytochrome b (mitochondrial DNA) and the D2 domain of the 28S ribosomal DNA. Maximum-parsimony and maximum-likelihood analyses showed that taxa formed two monophyletic groups, one clade comprising all species associated with Cupressaceae and Taxodiaceae hosts with the exception of Chamaecyparis, and the other clade composed of species associated with Pinaceae. Species infesting Cupressaceae and Taxodiaceae seemed to be specialized to particular host genera or even to be species specific, which was consistent with a taxonomic radiation following initial host adaptation. By contrast, Megastigmus species associated with Pinaceae appeared capable of shifting onto different congeneric species or even onto a new host genus, with their evolution apparently less constrained by plant association.We hypothesized that the Megastigmus group associated with Pinaceae may have a much higher invasive potential than that related to Cupressaceae. The study also confirmed the presence of invasive Nearctic species in the Palaearctic, and demonstrated the existence of a cryptic species complex.