Abstract Fishpond area of Sihcao, Tainan City, approximate 488 hectors, is a part of coastal wetlands of Taiwan. Fishponds can be found almost everywhere in the wetlands, readily forming a fragmented ecosystem. Previous studies on populations of small mammals in coastal wetlands of Taiwan are scarce. Disturbance types found in the study area include straying dogs, working farmers, tillaging of the fishponds, and typhoons, etc, which would probably reduce the abundance of small mammals. The resources such as shelter, vegetation coverage, insects and seeds would increase the abundance of small mammals. The seasonal changes of these environmental factors may in turn affect the population dynamics of small mammals. I monitored the monthly population fluctuation of small mammals and invertebrates in the fishpond habitats, 2008. Six species of small mammals and 106 species of invertebrates were found. The small mammal populations in the Hairy Beggar Ticks region were compared with those within the non-Hairy Beggar Ticks region. More small mammals were found in the Hairy Beggar Ticks region in the sampling period. The vegetation coverage of the former was higher than that of the latter. There was positive correlation between evenness of small mammals and temperature. No differences of the biodiversity of invertebrates were found between the regions in the year. Significant correlation existed between the sunshine duration and the richness of invertebrates. The correlation may be due to the change of photoperiod. There was no significant correlation between the richness of small mammals and that of invertebrates.