Pontellidae are representatives of the epipelagic marine biota, a community that inhabits the surface layer (SL) of the ocean. In SL habitat, they are exposed to ultraviolet (UV) and are constantly impacted by anthropogenic disturbances. Anthropogenic activities on the small islands could potentially influence the biodiversity and abundance of Pontellidae. This study aimed to reveal the biodiversity of Pontellidae on small islands (Jakarta Bay, Sikka Bay, and Ambon Bay). Datasets were collected from three sites, representatives of the urban small islands of Jakarta Bay and Ambon Bay, and one site of a suburban small island in Sikka Bay, Indonesia. Copepod samples were collected during September-November 2021. Sampling was done using a conical plankton net (mesh size 300mm) by horizontal towing. The result showed that the biodiversity of Pontellidae comprises 12 species belonging to six genera. Genus Labidocera has become the richest taxa (6 species). Biodiversity of Pontellidae at Sikka Bay > Ambon Bay > Jakarta Bay. However, the abundance of Pontellidae is slightly different with that at Sikka Bay > Jakarta Bay > Ambon Bay. These findings indicate that antropogenic activities and disturbances may affect the biodiversity and abundance of Pontellidae.