Waxy maize is one of the main fresh-eating maize types, and a mutation of the waxy gene causes the waxy character of maize grains. China is rich in waxy maize landraces, and Yunnan and its surrounding areas, are the place of origin and genetic diversity center of Chinese waxy maize. The six known waxy alleles of Chinese waxy maize are wx-D7, wx-D10, wx-Cin4, wx-124, wx-Reina, and wx-Xuanwei. The mutation sites of these alleles all occur in the coding region of the waxy gene, however, the mechanism by which the waxy characteristic is caused by the mutation in the regulatory region has only been reported rarely in maize. In this study, 405 waxy maize landraces from Yunnan were used as materials to identify the insertion and deletion of a large sequence fragment in the upstream ～3.5 kb regulatory region of the waxy gene by molecular marker detection. Three different waxy alleles were identifed in this study: wx-PIF/Harbinger, wx-hAT and wxElote2. These three types of mutations all represented transposons inserted into the regulatory region of the waxy gene. Wx-PIF/Harbinger was a 304-bp MITE class transposon insertion belonging to the PIF/Harbinger family, while wx-hAT was a 560-bp MITE class transposon insertion belonging to the hAT family, and wx-Elote2 was a 6560-bp LTR-like transposon insertion. In this study, the alleles were identifed for more than 70％ of the waxy maize landraces in Yunnan, which provids a basis for the utilization of these waxy maize landraces.