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Cogongrass [Imperata cylindrica (L.) Raeusch] is a wild plant species widely distributed throughout various tropical and subtropical regions. The wide distribution may lead to genetic differences among the species populations, which can be analyzed using particular molecular markers showing high mutation rate. This study aims to assess the genetic diversity of cogongrass in Java Island, Indonesia, and the genetic relationship among the populations based on psbA-trnH IGS. Plant samples were taken randomly from several places in Java, namely Purwokerto, Jetis Beach, Purworejo, Yogyakarta, and Ponorogo. The procedures involved genomic DNA extraction, amplification of psbA-trnH IGS, and sequencing of psbA-trnH IGS. The results showed that cogongrass populations in Java had a high genetic diversity with respect to haplotype diversity (h=1) but low genetic diversity in terms of nucleotide diversity (π=0.00658). This suggests a very close genetic relationship among cogongrass populations in the island, which can also be seen from the low values of genetic distances.