[Objectives]  To screen the whitefly Bemisia tabaci (Gennadius) genes that respond to infection by Beauveria bassiana in order to further elaborate molecular mechanisms underlying the immune response to fungal infection. [Methods]  High throughput sequencing technology was used in the transcriptome analysis of Bemisia tabaci 4th instar nymphs that were either infected, or uninfected (control), with B. bassiana. Differentially expressed genes (DEGs) and their functions, classifications and signaling pathways were analyzed using bioinformatic tools. [Results]  232 554 non-redundant Unigenes were identified, among which N50 and N90 were 1 153 bp and 260 bp in length, respectively. The average length of all Unigenes were 674 24 bp. Among the 1 166 DEGs (P<0.05) identified, 474 were up-regulated and 692 were down-regulated, and 405 are known to be involved in insect immune response. The identified Unigenes were enriched in 156 biological processes (66 402 Unigenes), 89 cellular components (27 645 Unigenes) and 154 molecular functions (73 417 Unigenes) by GO analysis. KEGG pathway analysis indicated that 1 145 DEGs were mapped to 309 distinctive pathways, and were enriched in 76 pathways. [Conclusion]  Four hundred and five genes that are possibly involved in the immune recognition and defense of whitefly nymphs against B. bassiana infection were sequenced. The results provide a bioinformatic data base for using entomopathogenic fungi as a biological control for whitefly.