Variation among 17 accessions of Citrullus lanatus from different geographic regions and interspecific relationships of six taxa of Citrullus and Praecitrullus were studied using electrophoretic patterns of their seed storage proteins. Globulins, the salt soluble proteins, represented the major fraction with their proportion varying between 56.6% and 67.0%. These were followed by albumins (16.6–20.8%) and glutelins (13.5–18.5%) with prolamins as the lowest (2.2–4.1%) of the four fractions. Two-dimensional gel electrophoresis under nonreducing conditions in the first dimension and reducing conditions in the second revealed disulphide-bonded subunit pairs of molecular weight 53, 52, 50 and 41 kDa, unlike the single subunit pair generally reported in different cucurbits, each consisting of a large and a small subunit. In the UPGMA dendrogram based on polypeptide patterns, the occurrence of C. lanatus var. lanatus, C. lanatus var. citroides and C. lanatus accession PI 482318 in one subcluster suggested that phylogenetically C. lanatus var. citroides and C. lanatus var. lanatus are closely related. The recently described annual wild species, Citrullus rehmii, occurred independently nearest to the subcluster of these cultivated and wild taxa. Citrullus colocynthis, the perennial wild species occurred farther from this cluster showing relatively more genetic distance from the watermelons. Praecitrullus fistulosus was outclustered and appeared genetically distant from all the Citrullus taxa; this supported its placement in a separate genus unlike its nomenclature as a botanical variety of watermelon or as a separate species of Citrullus proposed in certain earlier studies.