Among all orchids, Dendrobium sp. is considered to have high medicinal value. Dendrobium moniliforme and Dendrobium transparens have immense pharmaceutical, commercial potentiality. However, their fungal endophytes remain unexplored. Isolation and identification of thirteen species of endophytic fungi from the root of D. moniliforme as well as five species from the roots of D. transparens were done. The two endophytic fungi namely Aspergillus flavus and Trichoderma harzianum were common for both plant species. Antimicrobial assay was done against selected human pathogen both gram positive and negative Escherichia coli, Pseudomanas aeruginosa, Staphyllococcus aureus and Staphyllococcus epidermidis. The antimicrobial assay showed the significant role of endophytic fungi to inhibit the bacterial growth. Methanolic extract of DeMon VI and DeMon X were prepared to identify the bioactive compounds. Phenolic and 3-Eicosene,(E)-compounds were identified from extract of DeMon VI whereas Pentadecanoic acid, 14 methyle-, methyl ester and Diethyl Phthalate were identified from extract of DeMon X.