This paper reports the findings regarding morphology, DNA markers and fruit quality of Solanum muricatum L., a newly introduced fruit in Hazara University, Pakistan, and other locally grown members of the Solanaceae family. In this study, RAPD (Random Amplified Polymorphic NA) based PCR report on phylogenetic affinities of pepino with brinjal, chilies, potato and tomato was also included. Total genomic DNA was isolated and 120 arbitrary decamers were applied to the genomic DNA of all these species. Only five out of the 120 decamers produced 27 polymorphic loci with the range of 400 - 1400 bp. We observed the specificity of markers, and primer B-08 amplified 700 bp locus linked to Solanum muricatum L., (Pepino), which could be used to identify this particular species of this family. Cluster analysis was also performed using the DNAMAN software (version 5.2.2.0) against the bivariate data collected from the products of several decamers. The UPGMA (Unweighted pair Group Method with Arithmetic Mean) analyses depicted three distinct groups, i.e. group I sorted out brinjal-tomato, group II sorted out chili-potato and pepino sorted out into its independent group III. Though on the basis of morphological traits pepino clustered with tomato, its DNA analyses proved it as a distinct species, far more related to the tomato. Moreover a total six parameters in biochemical analysis were studied, which revealed that pepino is a juicy fruit with maximum 93.25% moisture. This study could be helpful to maximize the new crop pepino in Pakistan.