While it has been suggested that histone modification can facilitate animal responses to rapidly changing environments, few studies have profiled whole-genome histone modification patterns in introduced species, leaving its role in invasiveness unclear. Here, we screen genome-wide patterns of two important histone modifications, trimethylated Histone H3 Lysine 4 (H3K4me3) and trimethylated Histone H3 Lysine 27 (H3K27me3), in adult thorax muscles of a notorious invasive pest, the Oriental fruit fly Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), using Chromatin Immunoprecipitation with high-throughput sequencing (ChIP-seq). We identified active, repressed and poised promoters, featured by the occupancy of H3K4me3, H3K27me3 and bivalent histone modifications that were respectively annotated with unique genes key to muscle development and structure maintenance. In addition, we found H3K27me3 occupied the entire body of genes, with the average enrichment was almost constant. When comparing to the closely related indigenous Drosophila species, while we found highly conserved histone modifications patterns of distribution and function between the two species, we identified more genes and putative motifs modified by histone modifications that may regulate insect flight capacity and invasiveness compared to D. melanogaster. These findings provide the first evidence of histone modification signature in an invasive species, and will be useful for future studies of epigenetic regulation of invasiveness under global climate change.