The study was conducted on the individual chromosome identification in Gossypium darwinii (A_dD_d), G. klotzschianum (D_3k), G. davidsonii (D_3d), G. armourianum (D_2-1) and G. aridum (D₄) using a multi-probe fluorescence of in situ hybridization (FISH) system. Comparative analysis on their genetic maps with that of physical maps was made as well. The FISH probes used contained two sets of bacterial artificial chromosome (BAC) clones [one is specific to 26 individual chromosomes from A and D subgenomes of G. hirsutum (A_h and D_h) while the other is a D genome centromere-specific BAC clone 150D24], 45S and 5S rDNA clones. The results showed that all A_d chromosomes were marked with the 13 A_h chromosome-specific BAC clones, whilst all D_d, D_3k, D_3d, D_2-1 and D₄ chromosomes and chromosomal arms were identified with the 13 D_h chromosome-specific BAC clones and the D genome centromere-specific BAC. According to the homology within D subgenomes which are between A (D) genome and A (D) subgenome, the systematic nomenclature for individual chromosome in the five species was established. The chromosomes of A (D) subgenomes in G. darwinii were named as A_d01-A_d13 (D_d01-D_d13). The chromosomes in D_3k, D_3d, D_2-1 and D₄ were named as D_3k01-D_3k13, D_3d01-D_3d13, D_2-101-D_2-113 and D₄01-D₄13, respectively. Based on the successful identification for individual chromosomes, 45S and 5S rDNA were located to the special chromosomes and chromosomal arms for all five species. And there appeared chromosomal collinearity from the BAC clones among different species by comparing BACs positions, which suggested that the majority of chromosome segment homology may exist between D genomes and D subgenome. Moreover, as the genetic map and physical map were integrated, the orientations of genetic maps for D_d and D genomes of diploid cotton were established. The orientations of some of chromosomes in genetic maps (D_d03, D_d04, D_d06, D_d09, D_d10 and D_d12) were found switched. The SSR marker in the middle of linkage group 04 was corrected at nearby the end of chromosome 04 by FISH. The study will be helpful to establish a theoretical basis using the wild gene bank to exploit more genes aiming for cotton breeding and will provide powerful evidences both for the evolution of Gossypium and assembling the sequences of the obtained and as well the on-going whole genome sequencing projects of cotton.