The characteristics of arbuscular mycorrhizal fungal (AMF) community structure in various soil depths and growing seasons of watermelon (Citrullus vulgaris) grown in commercial greenhouses in Daxing of Beijing and Weifang and Laiyang of Shandong, China were investigated using both morphological identification and denaturing gradient gel electrophoresis. The sampled soils had been used for continuous greenhouse production of watermelon for 0, 5, 10, 15, or 20 years. Glomus claroideum was the dominant species in the greenhouse soils planted for 5, 10, and 15 years in Laiyang, while Glomus mosseae and Glomus etunicatum were dominant in the nearby open farmland soil. Sorenson’s similarity index of AMF community composition ranged from 0.67 to 0.84 in the soils planted for 5 years, and from 0.29 to 0.33 for 20 years among the three locations. Spore abundance, species richness, and the Shannon index were highest near the soil surface (0-10 cm) and decreased with soil depth, and higher in June and October than in August and December. Canonical correspondence analysis showed that available P and the number of years that soil had been used for greenhouse production were the main factors contributing to the variance of AMF community composition. It was concluded that the community structure of AMF was mainly influenced by soil available P and planting time of watermelon as well as by soil depth and seasonal variation in the commercial greenhouse. The characteristics of arbuscular mycorrhizal fungal (AMF) community structure in various soil depths and growing seasons of watermelon (Citrullus vulgaris) grown in commercial greenhouses in Daxing of Beijing and Weifang and Laiyang of Shandong, China were investigated using both morphological identification and denaturing gradient gel electrophoresis. The sampled soils had been used for continuous greenhouse production of watermelon for 0, 5, 10, 15, or 20 years. Glomus claroideum was the dominant species in the greenhouse soils planted for 5, 10, and 15 years in Laiyang, while Glomus mosseae and Glomus etunicatum were dominant in the nearby nearby open farmland soil. Sorenson’s similarity index of AMF community composition ranged from 0.67 to 0.84 in the soils planted for 5 years, and from 0.29 to 0.33 for 20 years among the three locations. Spore abundance, species richness, and the Shannon index were highest near the soil surface (0-10 cm) and decreased with soil depth, and higher in Jun e and October than in August and December. Canonical correspondence analysis showed that that P and the number of years that soil had been used for greenhouse production were the main factors contributing to the variance of AMF community composition. It was concluded that the community structure of AMF was mainly influenced by soil available P and planting time of watermelon as well as by soil depth and seasonal variation in the commercial greenhouse.