This study introduces the construction of the first intraspecific genetic linkage map of the A-genome diploid cotton with newly developed simple sequence repeat (SSR) markers using 189 F(2) plants derived from the cross of two Asiatic cotton cultivars (Gossypium arboreum L.) Jianglingzhongmian x Zhejiangxiaoshanlüshu. Polymorphisms between the two parents were detected using 6 092 pairs of SSR primers. Two-hundred and sixty-eight pairs of SSR primers with better polymorphisms were picked out to analyze the F(2) population. In total, 320 polymorphic bands were generated and used to construct a linkage map with JoinMap3.0. Two-hundred and sixty-seven loci, including three phenotypic traits were mapped at a logarithms of odds ratio (LOD) > or = 3.0 on 13 linkage groups. The total length of the map was 2 508.71 cM, and the average distance between adjacent markers was 9.40 cM. Chromosome assignments were according to the association of linkages with our backbone tetraploid specific map using the 89 similar SSR loci. Comparisons among the 13 suites of orthologous linkage groups revealed that the A-genome chromosomes are largely collinear with the A(t) and D(t) sub-genome chromosomes. Chromosomes associated with inversions suggested that allopolyploidization was accompanied by homologous chromosomal rearrangement. The inter-chromosomal duplicated loci supply molecular evidence that the A-genome diploid Asiatic cotton is paleopolyploid.