We sequenced the transcriptomes of liver and muscle samples of hybrid tilapia of different growth rate to identify differentially expressed genes. The tilapia were from F2 hybrid of F0 female Oreochromis mossambicus and F0 male O. niloticus. The samples with fast growth rate and low growth rate had different homozygous genotypes, AA and CC, respectively, at the most significant QTL marker related to growth performance.