In order to study mechanism of the differences of arbuscular mycorrhizal (AM)colonization rates among wheat genotypes，a pot experiment was conducted in two growing seasons from 2017 to 2019.Claroideoglomus etunicatum，Rhizophagus intraradices，Funneliformis mosseae，Acaulospora delicata were used for mixed inoculation，and the AM colonization was measured.Two wheat cultivars (YM14 and XHM)with contrast AM colonization were screened out and used for transcriptome analysis.The response of four types of genes (transcription factors，transporters，enzymes and other genes)that previously reported to be involved in AM symbiosis formation to AM colonization were focused.The study aimed to explore the molecular mechanisms of the genotypic differences of wheat in AM colonization.The results showed that the AM colonization rate of the cultivar YM14 was significantly higher than that of XHM，and the difference was more than 7 times.Three types of transcription factor family genes such as GRAS，AP2 and MYB were detected，most of which were up-regulated by AM colonization，but only 2 MYB transcription factor genes had distinct different responses to AM colonization between the two cultivars；Four types of transporter genes，including ABC transporter gene，phosphate transporter，sucrose transporter and ammonium transporter gene，were detected to respond to AM colonization.Among them，19 ABC transporter genes responded most strongly to AM colonization，and most of them had different responses to AM colonization between the two wheat cultivars；12 types of enzyme-encoding genes were detected to respond to AM colonization，of which 24 genes had differential expression more than 16 times，3 E3 ubiquitin ligase genes，1 subtilisin-like protease genes，6 cytochrome P450 family genes，and 2 serine carboxypeptidase genes had different responses to AM colonization between the two wheat cultivars；in addition，five other gene types involved in mycorrhizal symbiosis were detected，and 106 genes significantly responded to AM colonization，of which 3 F-box family genes had different responses to AM colonization between the two wheat varieties.In this study，57 genes with significant differences in response to AM colonization in the two wheat cultivars were identified，and may play key roles in affecting the genotypic differences of wheat in AM colonization.