Camellia section Paracamellia of the genus Camellia (Theaceae) includes major woody oil crops in China and relative wild species as valuable genetic resources for breeding. However, the phylogeny and origin of C. oleifera and its relative species are still uncertain. In this study, the transcriptomes of 22 samples and plastomes of 19 samples were sequenced and assembled. Finally, the dataset of phylogenomic matrices was generated, including 982 and 326 single-copy orthologous (SCO) genes generated from transcriptomes data and the plastid matrix used for phylogenetic analysis. Please cite this article as doi: 10.1111/jse.12948.