Abstract: Understanding the genetic basis of phenotypes is of importance in evolutionary biology and for genetic improvement of economically valuable animals. The giant phenotype of the fighting fish, Betta splendens, provides a unique opportunity to explore the genetic architecture of overgrowth in body size. As such, we re-sequenced and analyzed the genomes of 54 fighting fish. Genome-wide F_ST and selective sweep analyses using 3 582 429 DNA variants revealed three genomic regions at chr1, chr9, and chr11 that were associated with the giant phenotype. With a total length of ~3.5 Mb, these regions showed high divergence between the giant and non-giant bettas. In contrast, no signature of selection was detected in the wild-type fish. Transcriptome analysis of brain and muscle samples from giant and normal bettas identified 14 candidate genes that were likely responsible for the giant phenotype. Overall, our data provide novel insights into the genetic basis of body size variation. The genome sequences, transcriptome sequences, DNA sequence variants, and candidate genes for body size provide valuable resources for further biological and evolutionary studies, as well as for rapid improvement in growth-related traits.