Neotropical highland streams have shown diminished ecosystem functioning after amphibian extirpation infected by the chytrid fungus Batrachochytrium dendrobatidis. The loss of amphibians could affect communities of aquatic insects co‐occurring in these streams in various ways. We examined patterns of species and genetic diversity of these communities and their evolutionary history along the chytrid expansion gradient to elucidate potential community responses.

Six streams over a 320‐km transect in Panama affected by chytrid expansion from west to east for up to 14 years, and two apparently chytrid‐free streams in the east.

Patterns of α‐ and β‐diversity were investigated at three hierarchical levels: genus, species and haplotypes. Genus identification was based on morphology, and putative species were inferred by grouping the DNA barcodes (749 cox1 sequences) with the GMYC method on all collected individuals of Ephemeroptera, Trichoptera, Coleoptera and Plecoptera.

A total of 96 genera in 43 families (9 orders) of insects were encountered. Genus‐level α‐diversity was higher in the easternmost streams, possibly due to a separate biogeographical history, whereas β‐diversity was constant along the chytrid expansion gradient. Community DNA barcoding resulted in 426 cox1 haplotypes and 154 putative species, most of them limited to single sites. High β‐diversity along the gradient at both species and haplotype levels argues against community homogenization by migration in the wake of amphibian declines. In contrast, phylo‐β‐diversity was low, indicating community similarity at deep levels.

Aquatic insect communities in this region are influenced by long‐term limited dispersion that generated high endemicity. The pattern persists mostly unperturbed after disease‐driven amphibian declines; hence, if indeed insects fill the niches vacated by tadpoles, they would originate from local communities rather than immigration. Given the unique evolutionary history and physical isolation of local assemblages, the ecosystem deterioration carries the risk of losing unique diversity.