The Gunung Omeh citrus (Citrus nobilis Lour.) is a local citrus growing throughout the citrus center of West Sumatera. However, the fruits available in the market are very diverse phenotypic. The purpose of this study is to classify the spread of citrus cv. Gn. Omeh derived from four districts based on genetic and morphological characters. The study was conducted from January to June 2016, with 21 of leaf and fruit samples collected from four Citrus District Regional Development farmers in the West Sumatera (Limapuluh Kota, Agam, Solok Selatan, and Tanah Datar). Besides that, control leaf samples derived from Budwood Multiplication Block/BPMT and Single Mother Tree/PIT were used. The morphological diversity both leaves and fruits were analyzed by Principal Component Analysis (PCA). The result showed that the level of genetic similarity in 23 samples of orange Gn. Omeh analyzed using two markers RAPD namely OPA 04 and OPA 018 which generate 24 bands, where 83.3% were polymorphic The resulting data were further analyzed by cluster analysis to observe groupings. Based on the dendrogram calculated according to UPGMA, 23 samples genetically are divided into two major groups. In the first group, there are two samples from Limapuluh Kota, while the remaining 21 samples are in second group. On the degree of similarity between 86.5–96%, PIT similar to the A1 plant and it belong to the same subgroup with S2, A5, T3, T5, S1. While BPMT similar to T4 plant, and it belong to the same subgroup with A4 and A3. Based on morphological characters at a 75% degree of similarity, the Gn. Omeh citrus in West Sumatra is divided into five groups, where the L1, T5, S5, and S2 plant sample belongs to the groups 1, 3, 4, and 5, respectively, while 18 others in Group 2. From the analysis of both genetic and morphological characters, it generates fairly high degree of variation among 23 samples. This shows that the diversity of the marketed is thought to be caused by the use of seed plants and crop cultivated management are diverse.