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A 1000-year-old marine solar saltern in Hainan Island, South China, is in the continuation of traditional skills involving mud soak and solarization for three days to accumulate salt, which is a unique process contributing to the selection of highly halophilic microbes related to salt quality and flavor. Herein, the successions of physicochemical properties and bacterial and fungal communities of muds from the saltern were investigated during the processing of mud solarization. The results showed that Na+, Cl−, Mg2+ and total nitrogen were the main factors in explaining the fluctuation of the fungal community, whereas the bacterial community was predominantly determined by Ca2+, total kalium and total phosphorus. During three days of mud solarization, the soil bacterial alpha diversity in the saltern was significantly lower than that of the surroundings, whereas the fungal alpha diversity showed an opposite trend. The bacterial functional groups with the same survival and adaptation strategies remained relatively stable, while the dominant functional type in fungi changed from monotropic to complex trophic mode. Additionally, some unidentified fungi species were increasingly found in mud. The abundances of Saitozyma , Solicoccozyma and Wallemia (Basidiomycota) increased and may contribute to the salt flavor through decomposing cellulose molecules into glucose due to their higher β-glucosidase activity, while the harmful fungal genera including Inocybe and Paraconiothyrium decreased obviously due to the stresses of salinity and solar exposure. These results showed that the traditional salt-making skills associated with mud solarization have selected a high abundance of beneficial halophilic microbes to increase the salt quality and flavor. Our findings not only reveal the underlying mechanisms for the long-history salt-making skills of this 1000-year-old unusual cultural heritage but also are highly valuable for bioprospecting to develop novel halophilic bacteria and fungi for modern chemistry industries. [Display omitted] • Mud-solarization is a critical skill for the selection of highly halophilic microbes. • Successions of bacterial and fungal communities are revealed during the mud-solarization. • Bacterial functional groups with the same survival and adaptation strategies remain stable. • The dominant functional type in fungi changes from monotropic to complex trophic mode. [ABSTRACT FROM AUTHOR]