Abstract: Background and Objective: The assessment of the genetic diversity of new inbred lines has proven significant to the improvement of maize varieties. The objective of the study was to evaluate the diversity and relatedness of new Indonesian elite maize lines. Materials and Methods: Genetic diversity of 48 Indonesian elite maize lines was studied using six SSR markers. Some parameters were estimated including genetic relationship and genetic diversity. Genetic relationship was assessed using Jaccard’s similarity coefficient and was used to draw a neighbourhood-joining tree (NJT) by circle cluster using MEGA-pc software. Principal coordinate analysis (PCoA) was used for the estimation of genetic diversity. Results: All SSR loci detected in all genotypes were polymorphic. The population in this study is diverse as estimated by its polymorphic index coefficient (PIC). Population of 20 Indonesian maize lines was divided into 3 sub-groups, whereas 28 of mutant population was clustered into 7 sub-groups. Conclusion: SSR marker is a meaningful marker for genetic diversity study of Indonesian maize core collection. The forty-eight Indonesian maize genotypes were clustered into three major groups. These findings can be used in breeding methods for the development of populations.