Breed selection for commercial goat is needed for production efficiency, growth trait alteration, and improved livestock quality. Boer goat is famous for its stable production performance, fast growth rate, and high meat production. Detecting selective signatures in its genome can elucidate selection mechanisms for its economic and adaptive traits. In this study, 1,122,858 InDels were identified based on the whole genomes of 46 Australian Boer goats and 81 worldwide local goats. FST was used to identify the candidate selection signatures in 127 goats. A total of 11229 InDels were obtained from the top1% of all inDels, and 1239 candidate genes were annotated. A total of 1193 and 476 candidate genes were involved in 4726 GO terms and 299 KEGG pathways, respectively. Many genes were related to muscle development (MEF2C, MAPK14, TMOD1 etc.), reproduction (SRD5A1, FBXW11, DMRT1 etc.), immunity (CD200, SGK1, IL17RB etc.) and metabolism (INSR, STXBP3, H6PD etc.). The results provide novel and important insights into the genetic basis of selection in Boer goat and may be useful for goat molecular breeding.