The anamorphic genus Phoma includes many important plant pathogens. The classification of the Phoma species based on morphology is very difficult as they reveal multiple “species-specific” characters. Therefore an attempt has been made to describe taxonomical key and illustrate the cultural and morphological charcters ie. Growth and pigmentation of cultures, shape and size of pycnidia, condia, chlamydospores and sclerotia, of fourteen agriculturally important species of Genus Phoma to provide an authentic identification protocol to the end users.  The genetic relatedness among the twenty seven isolates representing fourteen Phoma species was also evaluated based on Randomly amplified polymorphic DNA (RAPD) and Inter simple sequence repeat (ISSR) markers. RAPD showed more polymorphism within particular Phoma species by seprating them into three clusters, whereas based on ISSR markers, isolates were grouped into five clusters and showed more polymorphism within different Phoma species. ISSR primers were also able to separate the Phoma species on the basis their section viz. Peyronellaea, Phoma, Phyllostictoides and Pilosa. Only one species, P. gardeniae belongs to section Paraphoma was not cluster separately. Overall, ISSR markers were found a much more efficient tool to differentiate variability among the different isolates of Phoma species.