Fish glue prepared from swim bladders has been used in China to glue wooden parts together since ancient times. It is also used as an important natural glue for wooden artifact and building restoration, musical instrument fabrication, as well as many other fields. Microorganism contamination is a major concern for fish glue preservation. In this research, fish glue was prepared from swim bladders using two methods, namely, heat treatment and enzymatic hydrolysis. Then, the molds that germinated in both samples were analyzed. Light microscope and scanning electron microscopy (SEM) observations of the molds’ hypha morphology identified Alternaria in both glue samples. The antimicrobial efficiencies of borax, sodium diacetate, and Antim AL-D (an organic/inorganic composite antimicrobial) were then compared. The results demonstrated that all antimicrobial agents in the research effectively inhibited Alternaria germination in both fish glue samples. A 0.3% (by weight) solution of Antim AL-D was sufficient for preserving fish glue. As for borax and sodium diacetate, the addition of a minimum of 1.0% was adequate to inhibit Alternaria growth. Results also revealed that the addition of Antim AL-D minimally affected the shear strength of glued wooden parts.