Bemisia tabaci is a species complex consist of about 40 cryptic species. This species is also a vector of at least 100 begomovirus including Tomato yellow leaf curl virus (TYLCV). TYLCV transmitted by B. tabaci in a circulative propagative manner but its molecular mechanism is remain unclear. We investigate the transcriptional response of B. tabaci MED to TYLCV infection using next generation sequencing (NGS) analysis. In total 16757 differentially expressed genes between viruliferous and non-viruliferous whiteflies were analyzed. Among them 289 transcripts found significant, where 116 up-regulated and 173 down-regulated. Our results reveal the whitefly-TYLCV relationship and provide important molecular information about virus transmission of vector insects.