AbstractSpecies of stalk‐eyed fruit flies, in the genera Pelmatops Enderlein and Pseudopelmatops Shiraki, have a distinct head structure with eyes located at the ends of stalks, setting them apart from other tephritids. Despite their unique morphology, the intraspecific variation of morphological and behavioural traits in these flies is still not well‐studied, leaving some questions about species definition unresolved. To address this, we conducted a study combining morphological evidence, behavioural studies, and molecular analyses. Our findings revealed male polymorphism in stalk‐eyed fruit flies for the first time, with four morphotypes observed in Pe. fukienensis and three in Pe. ichneumoneus and Ps. angustifasciatus. These morphotypes differ in eyestalk length, wing pattern, and the presence of projections or spikes at the ends of the compound eye. We also propose phylogenetic and phylogeographic implications for the group based on new molecular evidence, along with our observations of courtship and mating behaviours between previously recognized different species. Our study examined four nominal species (Pe. ichneumoneus and Pe. tangliangi, Ps. angustifasciatus and Ps. continentalis) and revealed rich evolutionary interactions within this group. Based on the results, we propose the synonymy of Pe. tangliangi Chen with Pe. ichneumoneus (Westwood) and Ps. continentalis Zia & Chen with Ps. angustifasciatus Zia & Chen.