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Mud shrimp Austinogebia edulis, an economically important sea food, has been protected in marine protected areas (MPAs) that are established in the western coast of Taiwan. However, there was no significant improvement in the abundance of A. edulis in MPAs in the last ten years. As benthic organisms in coastal wetlands, mud shrimp have ability to accumulate perfluorobutanoic acid (PFBA), which has the highest detection rate and concentration among eight per-and polyfluoroalkyl substances (PFAS) in coastal waters collected from 12 sampling sites along the coastline of Taiwan, through sediment and water exposure. Therefore, we investigated the abundance of A. edulis and the concentrations of PFBA in the sediment simultaneously to have a preliminary understanding of the occurrence of PFBA in mud shrimp breeding conservation areas. Grid sampling was conducted at two mud shrimp breeding conservation areas (Wanggong and Shengang) to estimate the abundance of A. edulis based on the burrow openings counted in the 0.09 m2 in November 2025. Then, sediment samples were collected from locations where higher or no burrow openings were observed. Additionally, mud shrimp samples were collected from Wanggong mud shrimp breeding conservation area and near Shengang mud shrimp breeding conservation area to confirm PFBA in biota samples. The average concentrations of PFBA in the sediment samples from Wanggong and Shengang mud shrimp breeding conservation areas were 56.40 ng g−1 and 52.65 ng g−1, respectively. Average abundances of A. edulis estimated for the sediment sampling sites located in Wanggong and Shengang mud shrimp breeding conservation areas were 13 and 40 number m−2, respectively. Moreover, the PFBA concentration in mud shrimp samples collected from Wanggong mud shrimp breeding conservation area (52.9 ng g−1) was higher than those collected near Shengang mud shrimp breeding conservation area (23.5 ng g−1). Even though our results indicated that sediment environments with lower concentrations of PFBA might habitat more mud shrimp, frequent investigation on the occurrence of PFBA and studies focusing on the bioaccumulation feature and potential impacts on mud shrimp were necessary to provide information for MPA management strategies and the transfer and bioaccumulation of PFASs through the food chain.