Most wetlands worldwide have suffered from extensive human exploitation. Unfortunately they have been less explored compared to river and lake ecosystems despite their ecological importance and economic values. This is the same case in Korea. This study was aimed to estimate the assemblage attributes and distribution characteristics of benthic macroinvertebrates for fifty wetlands distributed throughout subtropical Jeju Island in 2021. A total of 133 taxa were identified during survey periods belonging to 53 families, 19 orders, 5 classes and 3 phyla. Taxa richness ranged from 4 to 31 taxa per wetland with an average of 17.5 taxa. Taxa richness and abundance of predatory insect groups such as Odonata, Hemiptera and Coleoptera respectively accounted for 67.7% and 68.2% of the total. Among them Coleoptera were the most diverse and abundant. Taxa richness and abundance did not significantly differ from each wetland type classified in accordance with the National Wetland Classification System. There were three endangered species (Clithon retropictum, Lethocerus deyrolli and Cybister (Cybister) chinensis) and several restrictively distributed species only in Jeju Island. Cluster analysis based on the similarity in the benthic macroinvertebrate composition largely classified 50 wetlands into two major clusters: small wetlands located in lowland areas and medium-sized wetlands in middle mountainous regions. All cluster groups displayed significant differences in wetland area, long axis, percentage of fine particles and macrophyte composition ratio. Indicator Species Analysis selected 19 important indicators with the highest indicator value of Ceriagrion melanurum at 63%, followed by Noterus japonicus (59%) and Polypylis hemisphaerula (58%). Our results are expected to provide fundamental information on the biodiversity and habitat environments for benthic macroinvertebrates in wetland ecosystems, consequently helping to establish conservation and restoration plans for small wetlands relatively vulnerable to human disturbance.