This study was conducted to investigate the effects of partial substitution of dietary fishmeal (FM) by soy protein isolate (SPI) on lipid metabolism and gut microbiota of spotted seabass. A diet containing 30% FM formed the basal diet (FM), and two SPI diets were formulated in which 25% (SPI25) and 50% (SPI50) of FM were replaced by SPI. Each diet was fed to triplicates of fish for 56 days. The results showed that replacing dietary FM with SPI reduced triglyceride and cholesterol contents in the liver and serum, and the hepatic lipid droplets area was also decreased by dietary SPI inclusion. Furthermore, replacement of dietary FM with SPI markedly down-regulated the mRNA expression of genes involved in lipogenesis (srebpc-1c, fas, acc1, hmgcr, pparγ and chrebp) and lipolysis (atgl, hsl, pparα, and cpt1). Moreover, high-throughput sequencing analyses of gut microbiota revealed that dietary SPI inclusion dramatically decreased the Firmicutes/Bacteroidetes ratio. Overall, this study indicated that replacing 25-50% of dietary FM with SPI could reduce lipid accumulation in serum and liver of spotted seabass, which was associated with the suppressed hepatic lipogenesis and the remodeled gut microbiota.