The present study was carried out using twenty diverse speciality corn genotypes of QPM, sweet corn, pop corn and baby corn. The material was planted during kharif, 2015, at Rajasthan College of Agriculture, Udaipur. Observations were recorded for twenty yield contributing and ten morphological characters. Morphological observations, variability parameters and correlation coefficient were computed. DNA was isolated with CTAB extraction buffer method and isolated DNA was used as template for amplification of DNA using fifteen randomly selected decamer primers. It could be emphasized that sufficient variability existed in the material and characters like grain yield, stover yield, biological yield, TSS, test weight and cob height exhibited high estimates of GCV, PCV and heritability. Further some characters showed significant positive genotypic and phenotypic correlation with grain yield. Baby corn genotype HM-4 exhibited highest performance for grain yield while QPM genotypes (HQPM-1), sweet corn (Madhuri) and pop corn (Amber pop corn) turned out to be the best performers for grain yield/plant and most of the contributing characters. Molecular characterization through RAPD analysis revealed high polymorphism and marked genetic diversity among the speciality corn genotypes as also reflected by their morphological differences. Hence molecular characterization appeared to be precise, quick and effective tool in analyzing genetic diversity and identification of germplasm.