Plants from VNIIMK and VIR collections, their F1 and F2 progenies were assayed electrophoretically to determine inheritance of isozyme polymorphism and linkage relationship with genes controlling morphological traits in cultivated annual sunflower Helianthus annuus L. Chi-square goodness-of-fit tests verified segregation for 5 enzyme marker loci, including malate dehydrogenase (Mdh-2), glucose phosphate isomerase (Gpi-2), isocitrate dehydrogenase (Idh-2), esterase (Est-1), aconitase (Aco-1) and seven morphological loci: L (lemon colour ligulate flowers), T (anthocyanin colour of the whole plant), Ag (light colour of anthers), P (armour layer of pericarp), Ep (striped pigmentation of pericarp epidermis), Vs (increases leaf venation) and Ly (light yellow colour of ligulate flowers). Linkage was only determined for Est-1-Ly. Possible use of these data for the practical work is discussed.