This study aims to evaluate the morphological diversity of Kepel and analyse the genetical relationship towards Kepel distribution in Yogyakarta municipality based on fruit morphological. The research conducted in Yogyakarta municipality started in March-June 2019, and sample measurements carried out at in vitro culture laboratory and post-harvest laboratory, Agriculture Faculty, UMY. This study conducted using a purposive sampling method by specifying a distinctive characteristic of Kepel which has ripened, and one individual Kepel plant took ten physiologically of ripe Kepel. Data morphological observations presented by score form and then analysed the matrix similarity using SIMQUAL (Similarity of Qualitative Data) procedure. Matrix data grouping and dendrogram creation using Unweighted Pair Group Method Arithmetic Average (UPGMA) method in the Numerical Taxonomic and Multivariate System (NTSYS) program version 2.02i. The results prove that the diversity of Kepel fruit based on the qualitative and quantitative characterisation of Kepel morphology. The Kepel variety consists of fruit morphology such as shape, length, width, thickness, diameter, weight, maturity, flesh thickness, flesh colour, flesh texture, number of seeds, seed width, seed length, seed thickness, and seed diameter. Cluster analysis conducted on twelve individual Kepel in Yogyakarta municipality obtained five clusters with a similarity coefficient value of 0.44, namely group I:2 accessions, II:3 accession cluster, III:5 accession cluster, IV:1 accession cluster, and V:1 accession cluster.