In the present study, genetic linkage analysis was carried out to map the fiber color loci Lc(1) and Lc(2) on two brown cotton cultivars with SSR and EST-SSR markers in the reference map by F-2 segregation populations. The Lc(1) locus carried by Xincaimian6 (Gossypium hirsutum L.) was flanked by the marker NAU2862 and NAU1043 on the long arm of Chromosome 07, with genetic distance 7.8 cM and 3.8 cM, respectively. The Lc2 carried by Xincaimian 5 (Gossypium hirsutum L.) was flanked by the marker NAU5433 and NAU2968 on the short arm of Chromosome 06, with genetic distance 4.4 cM and 7.4 cM respectively. Moreover, the marker NAU3735 and marker NAU5434 co-segregated with the Lc(1) and the Lc(2) locus, respectively. The results of marker association studies with these two loci provides the basic information for the final isolation of these important genes in colored cotton, and these linkage markers also could facilitate application of marker assisted selection in the future.