The draft genome of *Gossypium raimondii*, a diploid cotton species, has been sequenced and assembled, providing insights into the evolution and genetic makeup of cotton. Over 73% of the assembled sequences were anchored on 13 G. raimondii chromosomes, and the genome contains 40,976 protein-coding genes, with 92.2% confirmed by transcriptome data. The genome exhibits evidence of a whole-genome duplication event approximately 13–20 million years ago and a hexaploidization event shared by eudicots. Syntenic blocks were identified, and the presence of paralogous genes in multiple blocks suggests substantial chromosome rearrangement. The G. raimondii genome is the only sequenced plant species with an authentic CDT1 gene family for gossypol biosynthesis. The study also highlights the importance of genes involved in cotton fiber initiation and elongation, as well as the role of transposable elements in genome size expansion. This work advances the understanding of cotton genome evolution and provides a valuable resource for improving cotton productivity and fiber quality.The draft genome of *Gossypium raimondii*, a diploid cotton species, has been sequenced and assembled, providing insights into the evolution and genetic makeup of cotton. Over 73% of the assembled sequences were anchored on 13 G. raimondii chromosomes, and the genome contains 40,976 protein-coding genes, with 92.2% confirmed by transcriptome data. The genome exhibits evidence of a whole-genome duplication event approximately 13–20 million years ago and a hexaploidization event shared by eudicots. Syntenic blocks were identified, and the presence of paralogous genes in multiple blocks suggests substantial chromosome rearrangement. The G. raimondii genome is the only sequenced plant species with an authentic CDT1 gene family for gossypol biosynthesis. The study also highlights the importance of genes involved in cotton fiber initiation and elongation, as well as the role of transposable elements in genome size expansion. This work advances the understanding of cotton genome evolution and provides a valuable resource for improving cotton productivity and fiber quality.