The gall-forming fly family Fergusoninidae, in association with a mutualist nematode, induces galls on Myrtaceae. Traditionally, each fly species has been thought to be host-specific and targets a particular site on its host plant. One host species may be host to as many as four fly species, each with different oviposition sites, giving rise to a range of gall types. Third-instar fly larvae possess a distinctive sclerotised ‘dorsal shield’ of unknown function that varies morphologically across the genus. We use a phylogenetic approach to examine the relationship of the dorsal shield morphology to other elements of this complex system. A phylogeny of 41 species, estimated using Bayesian analysis of mtCOI sequences, indicated a strong correlation between dorsal shield morphology and the gall type associated with the larva. We discuss possible functions of the dorsal shield, and other factors that may have led to their phylogenetic distribution. In addition, we have identified cases where fly species have formed galls on more than one host species. In some instances it is possible that these associations are an opportunistic response to artificial tree plantings.