Endophytic fungi synthesize a diverse set of enzymes and biomolecules with wide array of bioactivities. Thirty-five distinct fungal endophytes have been isolated from medicinal plants of Rutaceae and screened for their ability to produce various industrially important enzymes. Primary enzyme screening revealed that 65% of isolates produced L-Asparaginase, 62% of isolates produced cellulase, 60% of isolates produced amylase, 48% of isolates produced both lipase and pectinase, 45% of isolates produced laccase and 42% of isolates produced protease. Among the different enzymes screened, L-Asparaginase producing isolates were dominant and subjected to quantification using the nesslerization method. The endophytic isolates LCJ315, LCJ324, LCJ326 and LCJ335 were capable of producing high L-Asparaginase activity and their enzyme activity ranged between 7.58 U/ml to 8.84 U/ml. The four isolates were further subjected to molecular identification using 18S rRNA sequencing. The results were then subjected to BLAST analysis. The phylogenetic tree was created by MEGA software. The isolated endophytic fungal strains were identified as LCJ315 (Aspergillus sp.), LCJ326 (Colletotrichum sp.), LCJ324 and LCJ335 (Fusarium sp.). The fungal source of L-Asparaginase is preferred over other microbial sources of L-Asparaginase due to reduced side effects. Given the fact that L-Asparaginase is a crucial anticancer enzyme that is used as the initial therapy for acute lymphoblastic leukemia. Hence, the present study reveals that these endophytic fungal strains isolated from Rutaceae members can be used as an alternate source for L-Asparaginase production.