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The primary objective of the current research was to detect genetic variations within the Indonesian isolates of Cochliobolus heterostrophus collected from ecologically different places of the country at molecular level using PCR-RFLP analyses. The primer pair of NS3 and NS6 produced amplification fragment in all of the isolates tested. A single fragment of estimated 907 bp was observed in the PCR product pattern. RFLP analysis of the PCR product employing three restriction enzymes, HaeIII, HhaI, and RsaI, respectively, did not reveal intraspecific variations within the fungus. Similarly, nucleotide sequences of portion of small subunit of the ribosomal DNA gene of two of the isolates collected showed no appreciable differences, indicating the absence of genetic diversities among the isolates tested. A phylogenetic tree was constructed and the Indonesian C. heterostrophus, represented by SM-1 isolate, was found to be phylogenetically located near C. sativus, a closely related species.