The grass genus Chionochloa in New Zealand exhibits a high degree of mast seeding synchronised across species and habitats. Masting appears to be maintained by a predator satiation mechanism involving three pre-dispersal seed- and flower-feeding insects. It is not clear how important each of the three insects is in favouring the masting strategy. An undescribed cecidomyiid fly (Diptera: Cecidomyiidae) may be particularly important, since its conspicuous larvae are found throughout the South Island of New Zealand on many Chinochloa species. Despite the wide distribution of the larvae, it is not clear whether they are conspecific. Since the species is undescribed and adults are rarely seen, there may be different species on different host plants or in different geographic areas. We used Inter Simple Sequence Repeats (ISSRs) to determine whether cecidomyiid larvae found in four different areas in the South Island and on four species of Chionochloa exhibited molecular variation consistent with the presence of a single species of fly. Cluster analysis using Unweighted Pair-Group Method using Arithmetic averages (UPGMA) based on 38 ISSR fragments showed no clusters based on either host plant or geography. Analyis of Molecular Variance (AMOVA) analyses showed statistically significant differentiation among both host populations and geographic populations, but most of the molecular variation was explained by individual variation within geographic regions and host-plant populations. Thus, the molecular variation in the cecidomyiid larvae suggests the presence of a single species of cecidomyiid. Our data, combined with previous population surveys, suggest that the cecidomyiid is the most widespread of Chionochloa seed predators and may provide the selective benefit for the synchronous flowering observed among different Chionochloa populations in New Zealand.