Pertanika J. Trop. Agric. Sc. 42 (4): 1273 - 1288 (2019) TROPICAL AGRICULTURAL SCIENCE Journal homepage: http://www.pertanika.upm.edu.my/ Article history: Received: 9 April 2019 Accepted: 19 August 2019 Published: 13 November 2019 ARTICLE INFO E-mail addresses: oyelakinas@funaab.edu.ng (Abiodun Sunday Oyelakin) davidolabiyi@gmail.com (David Omobolaji Olabiyi) wanglihao@caas.cn (Lihao Wang) caoyacong@caas.cn (Yacong Cao) emmaidehen@yahoo.com (Emmanuel Ohiosimnuan Idehen) * Corresponding author ISSN: 1511-3701 e-ISSN: 2231-8542 © Universiti Putra Malaysia Press Genetic Diversity of Capsicum L. Accessions from South West Nigeria using Simple Sequence Repeats (SSR) Markers Abiodun Sunday Oyelakin 1 *, David Omobolaji Olabiyi 1 , Lihao Wang 2 , Yacong Cao 2 and Emmanuel Ohiosimnuan Idehen 3 1 Department of Pure and Applied Botany, Federal University of Agriculture, Abeokuta, P.M.B. 2240, Abeokuta, Ogun State, Nigeria 2 Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, People Republic of China 3 Department of Plant Breeding and Seed Technology, Federal University of Agriculture, Abeokuta, P.M.B. 2240, Abeokuta, Ogun State, Nigeria variance (AMOVA). The sum of 208 alleles was detected with an average value of 12.24 alleles per locus for each accession. Genetic diversity was high in all loci with the mean value ranging from 0.23 to 0.77. The result of AMOVA showed that 2 % of the genetic diversity was due to interspecifc variations while 98 % of the diferences were due to intraspecifc variations among accessions. The results of cluster analysis showed clearly high genetic similarity coefcient at > 71 %. The intraspecifc and interspecifc genetic relationships observed could be an integral part of the useful tools for genetic improvement of the genus Capsicum ABSTRACT Pepper (Capsicum L.) is a widely consumed vegetable in South West Nigeria because of its nutritional and medicinal potentials. This study is aimed at evaluating genetic diversity among 30 pepper accessions collected from diferent pepper-growing areas in South West Nigeria using SSR markers. Amplifcation potentials and bands clarity were considered for selecting 17 among 29 SSR markers screened. Genetic diversity was evaluated using principal coordinates analysis (PCoA), cluster analysis (CA), and analysis of molecular