The Banggai cardinal fish (Pterapogon kauderni, BCF) is an endemic ornamental fish species native to the Banggai Archipelago. Due to trade activities, this species has been introduced to various non-native waters, including Gilimanuk Bay, Bali, where it has successfully survived, grown, and reproduced, indicating that the ecosystem is suitable for its habitat. This study aimed to analyze the population distribution of the BCF in Gilimanuk Bay and to assess the environmental parameters that influence its habitat preference. Fish population data were obtained through a visual census using the belt transect method at 14 stations, grouped by location: inner Bay, southwest Bay, and Mouth Bay. Habitat characteristics data, including water depth, substrate, current, and waves, were collected using a remote sensing approach and a hydrodynamic model. The research revealed that the preferred habitat of BGF in Gilimanuk Bay was in the southwest part of the Bay, at a depth of 2–3 meters with low waves and weak currents, which was the initial introduction site of the fish. These areas also represented the most sea urchin-populated regions, and the most BCF-preferred habitats were found. Although sandy substrate is the broadest type of bottom in the sea, the BCF prefers coral rubble substrates, indicated by the highest preferences index value of 3.97, which are also suitable habitats for sea urchins.