Riau is one of the centers for pineapple production in Indonesia and harbored many local cultivar that have been cultivated for generations. The purpose of this study was to investigate the genetic diversity and genetic similarity between local cultivar in Riau based on RAPD (Random Amplified Polymorphic DNA) markers. Diversity analysis was carried out on ten local pineapple cultivar from five districts, namely Kampar, Indragiri Hilir, Siak, Bengkalis, and Dumai, using 11 RAPD primers. The PCR amplification result of the 11 RAPD primers selected generated a total 77 loci and the percentage of polymorphic loci was 96.42%. The high value of percentage of polymorphic loci reflected high diversity of pineapple in Riau propince. The values of genetic similarity coefficient of the pineapple genotypes in Riau Province ranged from 53% to 91%. The UPGMA dendrogram displayed that the Queen and Smooth Cayenne cultivars were separated in different cluster, while the Gemilang cultivar (GT) was placed between the Smooth Cayenne and Queen groups. This finding confirmed that Gemilang cultivar was the result of the natural crossing pollination between Smooth Cayenne and Queen pineapple.
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