We crossed a doubled haploid line of the turnip Brassica rapa cv. ‘Iyo-hikabu’, which is pigmented with anthocyanin, with a Chinese cabbage inbred line, ‘Y54’, which lacks anthocyanin pigmentation. The presence and absence of anthocyanin pigmentation was segregated 79: 27 in the F2 population, suggesting monogenic control. A bulked segregant analysis was conducted with random amplified polymorphic DNA (RAPD) markers. A total of 480 primers were used to screen a pair of bulked DNA samples of the F2 plants. We found five RAPD markers closely linked to the pigmentation locus. A partial linkage map around the pigmentation locus was constructed with four RAPD markers, two simple sequence repeat (SSR) markers, and one cleaved amplified polymorphic sequence (CAPS) marker. A 0.84-kb fragment amplified by a random primer, OPU10, was cloned, sequenced, and then converted into a CAPS marker (OPU10C). This CAPS marker was mapped at a distance of 4 cM from the pigmentation locus in the partial linkage map and was also mapped in linkage group R07 of the previously reported reference map of B. rapa. This locus is independent of the previously reported anthocyanin-regulating anl locus mapped in R09. We named the locus Anp. The locus will be useful in plant breeding and genome characterization in B. rapa.