During study of endophytic fungal diversity in tropical region, a new species of Arthrinium was isolated from healthy petiole of Jatropha podagrica. It is characterized by aseptate, dark brown, circular, lenticular conidia with hyaline margin, broad, hyaline conidiophores with numerous brown septa and ampulliform–lageniform conidiophore mother cells. The new species superficially resembles A. phaeospermum and A. saccharicola in having circular lenticular conidia, but differs in conidia and conidiophore size, and shape of conidiophore mother cells. Phylogenetic study using sequence analysis of ITS region (ITS1–5.8S–ITS2) separates the new species (A. jatrophae) from other related species of Arthrinium.