Plants harbor diverse fungal communities both on their surfaces (epiphytic) and inside of plant tissues (endophytic), and these fungi play important roles in plant health and vigor. However, comparisons of epiphytes and endophytes have rarely been performed. In this study, the soil, epiphytic and endophytic fungal assemblages of greenhouse-grown tomato plants were extensively examined and compared by Illumina sequencing of 18S rRNA amplicons. The fungal communities differed in both size and composition. The soil communities were the richest and most abundant, while the endophytes showed the lowest richness and diversity. The diversity of endophytes also differed in different tissues, with the highest diversity occurring in the roots. In both the epiphytic and endophytic samples, the majority of fungi corresponded to ascomycetes, among which Sordariomycetes, Dothideomycetes and Eurotiomycetes were the most frequent classes. The major non-ascomycete fungi were associated only with the class Exobasidiomycetes (Basidiomycota). At the order level, the epiphytes showed similar distribution patterns in the stems and leaves, but among the endophytes, distinct fungal orders were enriched in different tissues. Capnodiales was recorded as a major fungal group in the stems, leaves and seeds, and Saccharomycetales was specifically enriched in the pericarp and jelly around seeds. The present data suggested that different drivers shaped epiphytic and endophytic fungi communities and deepened our knowledge of the complex plant-fungus interaction in tomato.