Waterlogged wood from shipwrecks often displays bacterial or soft-rot decay. Cryo-sectioning and scanning electron microscopy indicated that the wood recovered from the Tektaş Burnu shipwreck was undergoing extensive degradation caused by erosion bacteria, tunnelling bacteria, and marine borer activity23. Wood samples from the rostrum of an excellent workmanship were analysed by 16S rRNA gene-based community sequencing techniques, revealing the presence of Pseudomonas spp., Sphingomonas spp., Xanthomonas spp., Marinobacter spp. and Desulforudis audaxviator24. Microbial decay is also a problem that was encountered in the preservation process of King Henry VIII’s Tudor Warship, the Mary Rose. Alicyclobacillus and Acidiphilium spp. were detected in this particular setting (66% and 34% of the communities, respectively). In addition, clone-library based 16S rRNA gene analyses indicated the presence of Acidobacteria and Bacteroidetes25. While samples collected from the Nanhai No. 1, the genera Idiomarina, Aquiflexum, Gracilibacillus, Bacillus, Halomonas, Marinobacter, Alicyclobacillus and Azoarcus were the main bacterial taxa. One possible reason for the differences of bacterial community in these cases is the different conditions of preservation. Although the shipwreck was stored in a tank with seawater, the upper deck has been exposed to the air. This brief increase in available oxygen may promote the growth of these dominant bacteria. Soft-rot decay seems to play the largest role in the deterioration of the shipwreck at present. Although a number of fungal genera were detected in wood from the Nanhai No. 1 shipwreck, the Fusarium genus was dominant in all samples and accounted for more than 90% of the total fungal communities.