Background The symbiotic bacteria occurring naturally in the cultivation bags of edible fungi during the mycelial growth is a huge resource to be explored. It is of significance to analyze the community structure and succession of symbiotic bacteria at the different growth and developmental stages of edible fungi and isolate growth-promoting strains that have an essential relationship with cultivation cycle, and traits and yields of fruiting bodies. Results In all samples from cultivation bags of Hypsizygus marmoreus, 34 bacterial phyla were detected, and Firmicutes was the most abundant bacterial phylum (78.85%). Serratia genera increased exponentially in cultivation bags in the matured period reaching the peak abundance of 55.74%, and became the dominant symbiotic flora. The most eye-catching strain was Serratia odorifera HZSO-1, and its quantity increased with the amount of hyphae of H. marmoreus. The results also verified that S. odorifera HZSO-1 was a symbiotic bacterium residing in the hyphae of H. marmoreus, and can promote the growth and development of H. marmoreus, shorten the fruiting cycle by 3–4 days, and increase the fruiting body yield by 12%. Conclusions This study was a pioneering demonstration of the community structure of symbiotic microbiota and its potential micro-ecology function in the growth and development of edible fungi and will lay a theoretical foundation of bacteria-mushroom interaction.