A total of 616 fungal isolates were obtained from 1600 segments of leaves and stems of the medicinal plant Anisomeles malabarica during four seasons (2009-2010). Fourteen different morphospecies were isolated: Botryodiplodia theobromae, Colletotrichum dematium, Pestalotiopsis microspora, Phoma betae, Phomopsis arnoldiae, Phomopsis stipata, Phomopsis sp., Phomopsis tersa, Phyllosticta murnadensis, Septoria sp., Penicillium sp., Nigrospora sp. and sterile forms. Phomopsis spp. was the most dominant and frequently isolated taxon. Colonization frequency (%) differed significantly between the seasons. The total colonization frequency of endophytes during south-west monsoon comprised young leaves 6.6%, mature leaves 15.7%, young stems 3.6% and mature stems 13.4%; north-east monsoon comprised young leaves 4.3%, mature leaves 16%, young stems 7% and mature stems 15.9%; winter comprised young leaves 14%, mature leaves 21.7%, young stems 12.5% and mature stems 17.1%; summer comprised young leaves 1.2%, mature leaves 4.4%, young stems 0.9% and mature stems 2.6%. The colonization rate was higher during the winter than in the monsoon and summer seasons. Moreover, the higher colonization frequency was found in mature leaves than in young leaves. The maximum relative percentage occurrence was coelomycetes (97.91%) followed by agnomycetes (1.33%) and hyphomycetes (0.76%).