Soil fungi are the predominant decomposers of soil organic matter (SOM). To manage SOM in tropical agricultural soils, it is important to understand the effects of agricultural management on fungal communities and their decomposition of organic matter. Our study site was located in a sugarcane plantation in Lampung Province, Sumatra, Indonesia. The goal of this study was to investigate fungal community response in decomposing sugarcane leaf litter to no-tillage and bagasse mulching by using Ion Torrent’s Personal Genome Machine (PGM). Our result indicated that bagasse mulching decreased genus level OTUs (85% identity threshold for clustering), whereas tillage system had no effect on the richness. However, IndVal analysis showed that no-tillage plot had the widest number and phylogenetic variety of indicator taxa. In contrast, bagasse mulching seems to encourage the growth of Basidiomycota. However, there were different indicators between no-till with bagasse mulch and till with bagasse mulch, indicating that different tillage practice may alter the fungal communities which were affected by bagasse mulching.