Sunflower (Helianthus annuus L.) being a cross pollinated crop, genetic adulteration is a vested problem and varietal descriptions are cumbersome. In order to identify genotypes and to establish phylogenetic relationships an investigation was carried on sunflower hybrids/parental lines/varieties using isoenzyme variation. The data on six isoenzymes were analyzed using Popgene software (Yeh, 1997). Genotypes which were morphologically closely related were found to be unrelated at the biochemical level. Hybrid KBSH-42 could be distinguished from the rest of the hybrids for the absence of pgi-2 and pgi-3. Alleles g6pdh-l, me-1 and skdh-3 served as markers in distinguishing the genotypes. Thus the results obtained could be used in fingerprinting the genotypes.