Abstract: Background and Objective: Moringa (Moringa oleifera Lam.) which also known as drumstick tree has been widely used for functional food in many countries and has spread out to almost all over the world including Indonesia. This study aimed to identify the genetic diversity of 30 genotypes from 10 populations of Moringa plants originating from several islands in Indonesia using SRAP molecular markers in combination with observations of morphological characters. Materials and Methods: In this experiment, the genetic diversity of Moringa from several islands in Indonesia was evaluated using Sequence Related Amplified Polymorphism (SRAP) molecular markers as well as morphological characters. A total of 30 genotypes of Moringa from 10 different islands in Indonesia were planted in 10 kg of polybags for 3-7 months to observe their molecular as well as morphological characters. For molecular analysis, 10 selected primers of SRAP were used. Results: The 70 polymorphic bands from 86 total bands (81.40%) were obtained and Polymorphic Information Content (PIC) values were 0.36 on average. The UPGMA analysis divided 10 accessions into 2 main groups which Java accession was grouped alone and separated from other accessions. The principle component analysis based on morphological characters divided them into 4 groups with Java accession consistently separated from others. Conclusion: Based on molecular and morphological analysis, accession of Java was the most distinct Indonesian Moringa accession suggesting the narrow distribution of this accession than others. Leaflets number, tuberous root number and color were among the most variables that influenced the distinction of Moringa accession from Indonesian archipelago.