This study optimised a single whitefly RNA extraction procedure and sequenced the transcriptome of four individual adult sub-Saharan Africa 1 (SSA1) Bemisia tabaci species (B. tabaci). Bayesian phylogenetic analysis of mitochondrion cytochrome I oxidase grouped the four whiteflies within the SSA1 clade while BLASTn searches on the four transcriptomes identified five endosymbionts that were predominant across all four SSA1 B. tabaci samples. The use of field-collected specimens means time and money will be saved in future studies using single whitefly transcriptomes in monitoring vector and viral interactions. The method in this study is applicable to any small organism where RNA quantity has limited transcriptome studies.