As the excavation progressed on land since November 2013, the upper deck of Nanhai No. 1 has been exposed to air, while the integral hull remained immersed in seawater. Non-woven fabrics were used to cover the areas directly exposed to air, and a spraying system was also used to maintain moisture. Meanwhile, borate buffer solution (BBS) was applied every week to prevent potential microbial contamination. However, in October 2014, fungal mycelia, in addition to salt precipitates, started to develop on some areas where the fabrics did not cover the wood appropriately. By using high-throughput sequencing techniques and culture-based methods, the aim of this study was to identify potential wood-degrading microorganisms that are responsible for the degradation of the Nanhai No. 1 shipwreck during storage. For this purpose, microbial community analysis was undertaken specifically on wood exposed to air. Furthermore, we investigated the enzymatic characteristics of the dominant fungi that were implicated in wood degradation. Finally, antimicrobial efficacy in inhibiting the growth of the dominant fungi was assessed with five kinds of biocides.