The ‘A-genome’ is an important cornerstone among cotton species. Its agronomic quality, underscored by continued cultivation across three millennia, and its increased genetic variation relative to cultivated AD tetraploid species make it a potential resource for cotton improvement. The A-genome harbors many traits that are lacking or compromised in the tetraploid species such as disease and insect resistance, high fiber strength, and excellent plasticity. Further, the A-genome is the evolutionary lineage in which seed trichomes acquired the physical properties that transformed them into economically important spinnable fibers, a charatacteristic carried over into the AD tetraploids (G. hirsutum and G. barbadense) that produce the world’s most important natural textile fiber. The A-genome genome sequence will facilitate the use of the A-genome diploid species in cotton improvement and research, but will also, alongside the D-genome genome sequence, provide critical insight in how to sequence the AD-genome effectively. Assembly of Gossypium arboreum genome sequence is underway based on over 150X Illumina short-insert paired end reads and nearly 300X clone coverage of long-insert Illumina (4kb) and 454 (19.5 kb) mate pairs. Preliminary assemblies will be integrated with a sequence-based Keygene physical map. The physical map is based on nearly 12X BAC coverage of the genome and covers 1700 Mb with a contig N50 of 900 kb. Sequence tags every 4-4.5 kb will aid in anchoring and ordering the genomic assembly. Data will be presented on the current status of the A-genome assembly focusing especially on the current challenge of integrating the sequence-based physical map.