Sequencing the cotton genome provides a wealth of genetic information, including insights into genome structure, diversity, species evolution, and gene variation. It also facilitates the identification of key genetic loci and biological processes associated with important agricultural traits. The Gossypium genus is classified into eight diploid genome groups (A–G and K), with phylogenetic analysis revealing that each group is monophyletic, consisting of closely related species. In recent years, substantial de novo sequencing and resequencing efforts have been undertaken, enabling detailed studies of the tetraploid AD genomes in allopolyploid cultivated cotton species and their diploid A and D sub-genome donors. However, there have been relatively few reports on the genomic analysis of other wild diploid cotton species. Here, we summarize results on the genome sequences of diploid cotton species from the B, E, F, G, and K genome groups, which were analyzed using various sequencing methods and techniques by two research groups. We found that 73.5% of the G. australe genome consists of repetitive sequences, which differ significantly from the repetitive sequences found in G. arboreum, G. hirsutum, and G. barbadense. Compared to G. raimondii, the G. australe genome shows closer collinearity with the G. arboreum genome and undergoes less genome recombination. Through comparative genomic analysis, we identified lineage-specific transposable element (TE) amplification in the K genome, which contributes to its larger size and also highlighted the relative conservation of gene content. Additionally, the genome sequence structure, assembly annotation, and TEs of several other wild cotton species, i.e., Gossypium longicalyx (F genome), Gossypium stocksii (E genome), and Gossypium anomalum (B genome), are described. By analyzing the genomes of various wild cotton species, this work lays a strong foundation for future studies on the systematic occurrence, species evolution, phylogenetic relationships, and genetic resources exploration in the Gossypium genus.