The fungal polyketide synthases (PKS) are responsible for the biosynthesis of several polyketide natural products, mycotoxins, pigments, etc. In the present times, we use computational tools to gain insight into polyketide natural products that may contribute to the metabolic versatility of this important phytopathogenic filamentous fungi. In total, we have identified 17 type-I PKS related gene clusters from the Macrophomina phaseolina genome. Among these 27 ketosynthase (KS) domains have been retrieved and used for the study. The study reveals that genome of M. phaseolina comprises non-reducing (NR), partially reducing (PR) and reducing (R) type of polyketides, and are clustered into three clades and several subclades. The phylogenetic analysis of KS domain sequences of M. phaseolina indicates that some PKS sequences are most closely related to polyketide natural product homologs such as lovastatin diketide, mycotoxins (fumonisin, citrinin and patulin) and pigment melanin. We also found eight orphan KS domains from three reducing PKS, i.e. MPH10374, MPH10375 and MPH10376. The study represents a potential novel source of industrially important polyketide natural products.