In this study,the WRKY gene fragment from a digital expression profiling of cotton root tissues infected by Fusarium oxysporum f.sp.vasinfectum (Fov) was used as a probe,a WRKY transcription factor gene was cloned from the roots of ‘Zhongmiansuo 12’ through the in silico cloning and RT-PCR,named as GhWRKY44(Genebank:KJ801807).Sequence analysis showed that the ORF of GhWRKY44 was 1 197 bp,encoding 398 amino acids.GhWRKY44 contained two conserved WRKY domains and one C2H2 zinc finger structure,and belonged to group I of cotton WRKY transcription factor.Phylogenetic analysis showed that GhWRKY44 closed to AtWRKY44.The GhWRKY44 expression was detected by Real-time Quantitative PCR(qRT-PCR) and the results showed that GhWRKY44 gene was predominantly expressed in resistant variety.With the duration of the treatment of Fov,the expression of GhWRKY44 increased firstly and decreased,then increased again.When the treatment time was over 3 hours,the level of GhWRKY44 expression reached the maximum in the resistant variety.However,the relative expression of GhWRKY44 was significantly lower and the response was later in the susceptible variety than that in resistant variety and the level of GhWRKY44 expression reached the maximum when the treatment time was over 6 hours.Both salicylic acid and jasmonic acid could induce the expression of GhWRKY44.After the treatment of salicylic acid,the level of GhWRKY44 expression increased rapidly and maintained at a high level.However,the expression of GhWRKY44 firstly increased and then decreased when induced by jasmonic acid.Compared with salicylic acid,the induced expression levels of GhWRKY44 were significantly lower than that of under jasmonic acid.The results demonstrated that GhWRKY44 may be response to pathogen and hormone stress in cotton.