| Summary: | Abstract Farm ponds, a valued habitat for freshwater organisms, are being negatively affected by the recent changes in the environment as well as anthropological activities. In these ponds, biodiversity researchers have tended to focus on species that prefer natural habitats and/or can be identified based on morphological characters. In contrast, this study focused on the insect family Chironomidae, which is widely distributed from clear to polluted waters of ponds, but is hard to identify morphologically as an aquatic larva. We adopted DNA barcoding and molecular species delimitation to identify every single specimen of quantitative collections. From bottom sediments of 17 ponds in summer in the Banshu Plain of Japan, a total of 62 species were delimited based on the DNA sequences of the mitochondrial COI region. Chironomid communities from these ponds were classified into four groups in a two‐dimensional ordination of multivariate analysis (NMDS). One of the dimensions was well correlated with the gradient of eutrophication, while another dimension was not clearly assigned to any general feature of the environmental gradient, but rice cultivation could possibly be involved.
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