Coscinium fenestratum is a medicinally significant critically endangered plant found in Western Ghats of India. The leaf spot and blight was observed in Kerala during 2021 with disease incidence of 40% in twenty assessed plants in 0.6 hectare. The associated fungus was isolated on PDA medium. A total of six morpho-culturally identical isolates were isolated and morphologically identified. Based on morpho-cultural features, the fungus was identified at genus level as Lasiodiplodia sp. which was further authentically confirmed as Lasiodiplodia theobromae by molecular identification with a representative isolate (KFRIMCC 089) using multigene (ITS, LSU, SSU, TEF1-α and TUB2) sequence analysis and concatenated phylogenetic analysis (ITS-TEF1-α-TUB2). Pathogenicity tests were also assessed in vitro and in vivo using mycelial disc and spore suspension of L. theobromae and the isolated fungus's pathogenic behaviour was confirmed after re-isolation and morpho-cultural features. Literature survey reveals that there are no reports of L. theobromae on C. fenestratum from all over the word. Hence, C. fenestratum is being firstly reported as new host record for L. theobromae from India.