Thrips (Thysanoptera) have been recorded as pollinators of various plant species, but they are mostly regarded to be of low ecological relevance. In Southeast Asia, thrips were recently discovered to pollinate flowers of several taxonomic sections of the pioneer tree genus Macaranga (Euphorbiaceae), which is particularly well known as an ant-plant, and for its importance in early forest succession. The lack of taxonomic treatment and of knowledge about systematic relationships among extant thrips, however, has prevented firm conclusions on the specificity of this plant-pollinator interaction. Here, results from sequencing of the mitochondrial cytochrome oxidase subunit support our previous morphospecies concept of Macaranga flower thrips, and confirm the genetic identity of five recently described species. They were remarkably all assigned to the genus Dolichothrips (Phlaeothripidae), which typically consists of phytophagous species. In addition, the molecular data revealed one cryptic species. A first phylogenetic tree of the Dolichothrips associated with Macaranga provides insights into their systematic position. In particular, we identify monophyly of all important Macaranga pollinator species, all species being largely specific to particular taxonomic host plant sections. Our results suggest a closely matched diversification of pollinating thrips with Macaranga trees. This adds a novel type of association to thrips pollinator-plant interactions, which have been so far documented as single-species interactions or generalist thrips species visiting multiple plant taxa.