Background The digestive tract of birds contains diverse microbiota that are essential for their health and survival, and these gut microbiota are influenced by a variety of factors. To compare the diversity in fecal microbiota of the same bird species in different environments, this paper collected feces of Little Egret (Egretta garzetta) and environmental (soil and water) samples from coastal salt water and inland freshwater areas to explore how fecal microbiota responds to different environments using 16S rRNA high-throughput sequencing methods. Results The main fecal microbiota from two sampling sites were similar at the phylum level. In terms of genus level, the dominant genera in feces from salt-water habitats (SWF) were Escherichia-Shigella (14.448%), Enterococcus (10.064%), Vibrio (7.812%), whereas there were Sporosarcina (18.241%), Citrobacter (11.987%), Acinetobacter (6.201%), Kurthia (5.725%) in feces from freshwater habitats (FWF). A few ASVs were sharedamong the egrets and the environmental samples in the two regions. The fecal microbiota between the two sampling sites showed no significant differences in α-diversity and were significant in β-diversity; there were no significant differences between the environmental microbiota diversity of the two sites. In contrast, most of the parameters reflecting α-diversity and β-diversity were shown to be significantly different between the fecal and environmental microbiota. In composition of microbiota function, the fecal microbiota of little egret and the environment microbiota were similar in relative abundances in the proportion of kegg level 1 functional pathways. But there were significant differences in some level 2 and level 3 functional pathways between the egrets from two habitats. Moreover, a portion of ASVs classified as opportunistic pathogens were detected in the feces of the egrets. Conclusions The results of this study indicate that there are differences in the fecal microbiota of the little egrets in different environments, and the differences are less affected by soil and water. Considering that Vibrio which was more common in the guts of marine fish, it is hypothesized that regional differences in fecal microbiota composition are related to changes in food types.