Seven isonitrogenous and isoenergetic experimental diets were formulated to investigate the effect of low molecular weight fish protein hydrolysate (FPH) in diets on growth performance, feed utilization and liver IGF-I mRNA levels in Japanese flounder (38.80 ± 1.11 g) fed with high plant protein diets. Fish meal protein was, respectively, replaced by 6% (FPH6), 11% (FPH11), 16% (FPH16), 21% (FPH21), 26% (FPH26) FPH of total dietary protein. FPH diets contained a constant high level of plant protein (690 g kg−1) from soybean meal. As a positive control diet, FM2 contained about 590 g kg−1 plant protein and 410 g kg−1 fish meal protein, while negative control diet FM1 contained about 690 g kg−1 plant protein and 310 g kg−1 fish meal protein. The expression levels of liver IGF-I mRNA were evaluated using real-time PCR normalized against the 18S rRNA gene. The results showed that moderate low molecular weight FPH (FPH11) improved growth performance and protein retention. Fish fed with FPH11 and control diet FM2 had similar growth and feed utilization, while high-level low molecular weight FPH did not improve growth performance and protein retention, and depressed liver IGF-I mRNA expression in Japanese flounder.