The variability of 14 landraces belonging to a Madrilean village historically specialized on melon cultivation, Villaconejos, was evaluated based on 58 quantitative and qualitative morphological traits. These landraces were compared to a reference array composed of 14 accessions which represented the main varieties cultivated in Spanish fields. Individual data related to plant, fruit, seed and phenology have been analysed using a multivariate analysis. This analysis showed intra- and inter-varietal diversity, as emphasized the most discriminant morphological traits in order to define similarities. Villaconejos accessions were morphologically distinct from the reference accessions (RA). Only the landraces belonging to Piel de Sapo market class showed common morphological affinities with the RA, grouping with them. The majority of Villaconejos traditional varieties clustered in five different groups, with no RA within, showing distinctive morphological singularities not described previously. Two of these groups showed some particularities in fruit traits, which are appreciated as quality marks for Spanish consumers. These results indicate that these accessions must be conserved as valuable genetic resources to enrich the Inodorus genetic bases for future breeding proposes worldwide. Furthermore, it should be considered the opportunity of promoting their cultivation under the shelter of a Protected Geographical Indication as a high quality melon. Finally, the discovering of such a high variability presented in a very small area, gives a clue for focusing, with an elevated probability of success, future surveys in similar ancestral European villages which in the past times, also supplied more populated cities with their farming products.