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Information on genetic diversity of Ganoderma spp. causing root rot disease in crops is important to develop a proper strategy for the control of Ganoderma disease. The objectives of this research were to study the genetic diversity of Ganoderma spp. associated with cacao and its shade trees (Albazia faltacaria, Swietenia mahogani, Adenathera microsperma and Leucaena leucocephala) by random amplified polymorphic DNA (RAPD) analysis. Fourty five samples of Ganoderma spp. were used in this research. The results showed that DNA amplification using 10 arbitrary oligonucleotide primers produced 220 DNA fragments showing polymorphisms. The cluster analysis showed that 45 number of Ganoderma samples had a high variability with the coefficient value ranged from 0.71 to 0.91. Further analysis using Winboot software showed that three groups of Ganoderma spp. had a high degree of confidence (>50 %), which were Ganoderma samples from sengon (Paraserianthes sp.) of Tasikmalaya, sengon (Paraserianthes sp.) of Palembang, and mahogany of Jember; whereas the other groups of samples had a low degree of confidence ( 50 %) yaitu kelompok Ganoderma spp. yang berasosiasi dengan pohon sengon asal Tasikmalaya, sengon Palembang, dan mahoni Jember; sedangkan pengelompokan lainnya menunjukk menunjukkan tingkat kepercayaan yang rendah (<50 %).

Analisis keragaman genetik Ganoderma spp. yang berasosiasi dengan tanaman kakao dan tanaman pelindungnya menggunakan Random Amplified Polymorphic DNA (RAPD) Genetic diversity analysis of Ganoderma spp. associated with cocoa and its shade trees using Random Amplified Polymorphic DNA (RAPD)