Land plants, in general, rely heavily on positive interactions with fungal endophytes for growth, disease resistance, and stress tolerance. Root colonization, isolation and tri-calcium phosphate (TCP) solubilizing activity of root endophytic fungi (REF) obtained from hybrid tomato (Lycopersicon esculentum Mill. var. TNAU CO3) plants grown in natural fields were examined. All field-collected tomato roots were positively colonized by DSE (dark septate endophyte) fungi. A total of 94 culturable fungal isolates belonging to 8 distinct orders, 9 genera, and 11 species were recovered and identified by morphological examination. In L. esculentum roots, the endophytic fungal colonization rate (CR%) was noticeably high (62.67%). Aspergillus niger was the dominant fungus with a relative abundance (RA%) of 23.4%, while A. niger, Cladosporium cladosporioides, and Fusarium oxysporum had the maximum isolation frequency (IF%). Furthermore, we evaluated the nature of the identified fungal isolates as endophytes by a pot study. Thus, 9 of 11 fungi colonized the test plant roots with clear intracellular structures, including Alternaria spp., C. cladosporioides, Colletotrichum spp., and F. oxysporum, which are DSE fungi. Furthermore, four REF were able to solubilize the TCP, with SI% ranging from 1.3 to 2.4%. This study's findings will help to improve our understanding of REF interactions and their potential ability to solubilize inorganic phosphate, as well as the application of these fungi to increase the development and productivity of diverse agricultural plants in sustainable agriculture.