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Despite the socioeconomic as well as ecological importance of small-scale fisheries in developing countries, there is a dearth of information on the state of artisanal fisheries in different regions of the tropical Indo-Pacific. In this study, catch patterns in small-scale artisanal fisheries within an area of high marine biodiversity in the western Pacific were analyzed using data gathered directly from the main fish market in Manado, North Sulawesi, eastern Indonesia. Of a total of 350 species identified among harvested fishes, the majority of species (ca. 90%) were closely associated with shallow reef habitats (<50 m), and open/deep-water species constituted a small proportion. There was a clear preponderance of relatively small (<50 cm) fish species among marketed fishes, with a steep decline in abundance of larger species, suggesting the possibility of overfishing. Faunal complementarity or distinctness between wet (November–March) and dry (April–October) season was lower for reef-associated fishes than for nonreef ones, reflecting the less-targeted nature of reef fisheries. Although relative catch patterns were broadly similar between wet and dry season, variability in catches as expressed by the variance of the truncated lognormal model was smaller in reef-associated than in nonreef species, indicating existence of year-round, relatively stable fishery activity centered on shallow reef environments. This finding points to the importance of reef habitats and their associated fish faunas for the artisanal fisheries of the tropical western Pacific.