We sought to investigate the nature of the microbial contamination of the shipwreck at two periods. In April 2015, two samples (NHI.1 and NHI.4) were taken using minimally invasive sampling techniques with sterile scalpels (Supplementary Fig. 2). These samples were collected from areas showing visible mycelia on the outside of the ship’s hull. In October 2015, four samples (NHI.8, NHI.9, NHI.11, and NHI.12) were collected using the methods described above. All samples were placed into 2 mL micro-centrifuge tube and brought to the laboratory in an icebox for subsequent microscopic observation and DNA extraction. The sampling locations on the Nanhai No. 1 ship’s hull are indicated in Fig. 1. Permission to sample was issued by the Marine Silk Road Museum of Guangdong. Yue Chen and Jie Liu from the Chinese Academy of Cultural Heritage (CACH) supervised the sampling process.