Abstract: The commercial fishery for coral reef fish for the aquarium trade has begun to change, at least in some parts of the world, from destructive methods such as cyanide and dynamite fishing to less‐destructive methods such as hand‐net fishing. However, data on the effects on wild populations of such relatively nondestructive methods is nonexistent. The Banggai cardinalfish ( Pterapogon kauderni ) is a paternal mouthbrooder living in groups of 2–200 individuals in the proximity of sea urchins ( Diadema setosum ). This fish has limited dispersal abilities because it lacks a pelagic larval phase, and it is believed to be endemic to the Banggai archipelago off the east coast of Sulawesi, Indonesia. Since its rediscovery in 1995, the Banggai cardinalfish has become a popular aquarium fish, and thousands have been exported—mainly to North America, Japan, and Europe. To study the effects of the aquarium trade fishery on wild populations of the Banggai cardinalfish, we performed a field study in which we quantified density, age distribution ( quantified as the ratio of numbers of juveniles to adults ) and habitat quality ( i.e., sea urchin density ) at eight sites in the Banggai archipelago. Through interviews with local fishers, we estimated the fishing pressure at each site and related this to data on fish density. We found a marginally significant negative effect of fishing pressure on density of fish and significant negative effects on group size in both sea urchins and fish. We did not find any effect of fishing on fish size structure. To our knowledge this is the first study to compare sites under different amounts of fishing pressure that has demonstrated the negative effects of the aquarium trade on wild populations of reef fish, despite the widespread use of relatively nondestructive fishing methods.