Abstract Background The fall armyworm, Spodoptera frugiperda (JE Smith) (Lepidoptera: Noctuidae), is a new invasive pest in Indonesia causing financial losses. S. frugiperda larvae hide in the leaf midrib all day. To overcome the hidden larvae, pathogenic endophytic fungi are needed. The objective of this research was to molecularly identify the endophytic fungal species from South Sumatra and determine the most pathogenic species against S. frugiperda larvae. Endophytic fungal identification was based on morphological and molecular characteristics. The molecular identification was based on gene sequential analysis of Intergenic Transcribed Spacer (ITS) 1 and ITS 4. Bioassay of the endophytic fungal species was treated against the 2nd larval instar of S. frugiperda. Result The results of molecular identification revealed endophytic fungal species consisted of Chaetomium sp. (GaTpeOi, JgTjPr, PiCrPga, and CaCjPga isolates), Aspergillus niger (L.) Van Tieghem (PsgTjPr, JgByU, and JaBuBys), Beauveria bassiana (Balsamo) Vuillemin (JgSPK, JaGiP, JaSpkPGA(2), JgCrJr, and JaTpOi (1) isolates), Curvularia lunata (Wakker) Boed. (JaGiPRB, CMTJP, JaMsBys, JaSpkPga(3), and JgTgSr isolates), Aspergillus flavus Link. (JgPWSR isolate), Penicillium citrinum Thom F 1539 (JaTpOi(2) isolate), and Metarhizium anisopliae (Metschn.) Sorokin (CaTpPGA isolate). All fungal isolates were deposited in the GenBank. The endophytic fungal species of B. bassiana (JgSPK isolate) caused up to (22.67%) mortality, C. lunata (JaSpkPga(3) isolate) caused (17.33%) mortality, and M. anisopliae (CaTpPga isolate) caused (8%) mortality of the pest’s larvae. First report of B. bassiana and C. lunata isolated from maize (Zea mays L.), while M. anisopliae was isolated from red chili (Capsicum annuum L.) as entomopathogenic endophytic fungi against S. frugiperda larvae in Indonesia. Conclusion The endophytic fungi species of B. bassiana, C. lunata, and M. anisopliae had potentials as entomopathogens of S. frugiperda.