ABSTRACTMulching is an important agricultural management tool for increasing watermelon productivity and land-use efficiency because it helps improve water use efficiency and reduce soil erosion. However, there is relatively little available information regarding the effects of long-term continuous monoculture farming on soil fungal communities and related fungal pathogens in arid and semiarid regions. In this study, we characterized the fungal communities of four treatment groups, including gravel-sand-mulched farmland, gravel-sand-mulched grassland, fallow gravel-sand-mulched grassland, and native grassland, using amplicon sequencing. Our results revealed that the soil fungal communities differed significantly between mulched farmland and mulched grassland as well as the fallow mulched grassland. Gravel-sand mulch significantly impaired the diversity and composition of soil fungal communities. Soil fungal communities were more sensitive to gravel-sand mulch in grassland than in other habitats. Long-term continuous monoculture (more than 10 years) led to decreased abundance ofFusariumspecies, which contains include agronomically important plant pathogens. In the gravel-mulched cropland, somePenicilliumandMortierellafungi were significantly enriched with increasing mulch duration, suggesting potential beneficial properties of those fungi that could be applied to disease control. We also found that long-term gravel mulching in continuous monoculture farming could potentially form disease-suppressive soils and alter soil microbial biodiversity and fertility. Our study provides insights into the exploration of novel agricultural management strategies along with continuous monoculture practice to control watermelon wilt disease by maintaining a more sustainable and healthier soil environment.IMPORTANCEGravel-sand mulching is a traditional agricultural practice in arid and semiarid regions, providing a surface barrier for soil and water conservation. However, application of such practice in monocropping systems may lead to outbreaks of several devastating plant diseases, such as watermelonFusariumwilt. Our results with amplicon sequencing suggest that soil fungal communities differ significantly between mulched farmland and mulched grassland and are more sensitive to gravel-sand mulch in grassland. Under continuous monoculture regimens, long-term gravel mulch is not necessarily detrimental and may result in decreasedFusariumabundance. However, some known beneficial soil fungi may be enriched in the gravel-mulch cropland as mulch duration increases. A possible explanation for the reduction inFusariumabundance may be the formation of disease-suppressive soils. This study provides insight into the need to explore alternative strategies using beneficial microbes for sustainable watermelon wilt control in continuous monocropping system.