Aphids are one of the famous agricultural pest insects in the world. Generally, these insects damage hostplants by sucking phloem directly and transmitting plant pathogen viruses indirectly. Aphis gossypii, (in the tribe Aphidini and the family Aphididae), which is polypagous species, shows various morphological characters due to adaptations to different host plants, geographic isolation, and genetic drift. It will be useful to understand the differences between cotton aphid and pea aphid (Acyrthosiphon pisum), of which genome was already sequenced and analyzed well. Here, we generated around 180x coverage raw data of A. gossypii genome using Illumina HiSeq4000 with two pair-end and two mate-pair libraries. First version of draft genome presents that total length is 357.44 Mbp (N50 is 472,772 bp and max length of scaffold is 2.71 Mbp), which is similar to genome length predicted by k-mer analysis (390.11Mb). Length of most of scaffolds (310,662 out of 319,177) is less than 500bp. In comparison to pea aphid genome (Acyrthosiphon pisum), genome length of A. gossypii is two-third (541.68Mb) and GC ratio (27.73\%) is similar to that of pea aphid genome (29.76\%). Number of ORFs predicted by AUGUSTUS is 16,462, which is smaller than that of pea aphid (36,970 ea). Interestingly, 2,488 InterPro terms were found only in A. gossypii, while 744 terms were in A. pisum, presenting that genome composition of A. gossypii is quite different from A. pisum. All these data including genome sequences will be available in Aphid genome database (http://www.aphidgenome.info/) for further comparative genomic analyses.