Abstract Flower color can be applied to landscaping and identification of the purity of seeds in hybrid production. However, the molecular basis of white flower trait remains largely unknown in Brassica rapa. In this study, an F2 population was constructed from the cross between 15S1040 (white flower) and 92S105 (yellow flower) for fine mapping of white flower genes in B. rapa. Genetic analysis indicated that white flower trait is controlled by two recessive loci, Brwf1 and Brwf2. Using InDel and SNP markers, Brwf1 was mapped to a 49.6-kb region on chromosome A01 containing 9 annotated genes, and among them, Bra013602 encodes a plastid-lipid associated protein (PAP); Brwf2 was located in a 59.3-kb interval on chromosome A09 harboring 12 annotated genes, in which Bra031539 was annotated as a carotenoid isomerase gene (CRTISO). The amino acid sequences of BrPAP and BrCRTISO were compared between two yellow-flowered and three white-flowered lines and critical amino acid mutations of BrPAP and BrCRTISO were identified between yellow-flowered and white-flowered lines. Therefore, Bra013602 and Bra031539 were predicted as potential candidates for white flower trait. Our results provide a foundation for further identification of Brwf and increase understanding of the molecular mechanisms underlying white flower formation in Chinese cabbage.