Smoke-induced seed germination has been discovered on a wide range of species. KAI2 was identified as the protein coding gene for the karrikins receptor, one kind of the active compounds that regulate seed germination. Most studies assumed that KAI2 is responsible for smoke-induced seed germination traits after its identified in Arabidopsis thaliana. In this study we explored the functional phylogenomic of KAI2 in a native species, Bouteloua gracilis, which have proved smoke effects on seed germination acceleration. We used RNASeq of four pools of seeds, and de novo transcriptome assembly to identify KAI2 homologs in B. gracilis. Further, we identified the KAI2 orthologs through the One Thousand Transcriptome project to trace the gene evolution path among species. Our results showed that even though there are three copies of KAI2 homolog, including two copies of KAI2 ortholog, there is no differential gene expression among these copies in response to smoke. This result indicated that KAI2 homologs are not responsible for the smoke effects in B. gracilis.