ABSTRACT Objective We sought to analyze the effects of fecal microorganisms on the basic fecal characteristics of fish in a recirculating aquaculture system. Methods Three main marine economic fish were selected based on economic value and main living habits. All samples were 1-year-old fish. The 16S ribosomal RNA high-throughput sequencing technology was used to study their fecal microorganisms. The basic characteristics of feces were determined by a texture analyzer. Results The fecal microbial relative abundance and diversity of omnivorous Turbot Scophthalmus maximus were higher than those of carnivorous Yunlong grouper (Kelp Grouper Epinephelus moara ♀ × Giant Grouper E. lanceolatus ♂) and Yellowtail Kingfish Seriola lalandi. The relative abundance of Veillonella, Bacillus, and Prevotella tended to increase with voluntary exercise. The stability of feces from Turbot, Yunlong grouper, and Yellowtail Kingfish tended to increase with the abundance enhancement of Firmicutes and Enterobacter and tended to decrease with the abundance enhancement of Bifidobacterium and Lactobacillus. Conclusions The fish habits appear to affect the composition of fecal microorganisms. The fecal microorganisms seem to affect the basic fecal characteristics.