Anthracnose symptoms were observed in the samples collected from the 39 infected plants of Bergenia ligulata (Wall) (family Saxifragaceae) along the Himalayan mountain ranges of India. Fungal isolates were recovered directly from the structures present on the lesions. Purified DNA from each isolate was amplified using the random amplified polymorphic DNA technique viz. recruiting the ITS1 and ITS4 specific primers. Amplification products visualized on agarose gel showed specific band pattern for each isolate. The mycotaxonomic characterization and phylogenetic interpretations showed the emergence of fungal species, Colletotrichum lillacola sp.nov. with genetic variance of 0.5 in internal transcribed spacer (ITS) region of rDNA from closely related species under geographically distinct region. The pathogen is having a lethal effect on the B. ligulata populations in India and solid containment measures should be imposed to restrict its spread throughout in its natural range ecologically, economically and pharmacologically as a precious host.