The paper presents the marker gene collection and the possibilities to use them in sunflower breeding programs. There are two classes of markers: morphological and physiological. The marker genes are in connection with colors of ligulate flowers, anther and pollen grains, shape of ligulate flowers, branching of the stem, pigmentation, seed characteristics. Five different sunflower inbred lines with marker genes were crossed between them, in order to identify new linkages. Between F2 progenies, double and triple recessive genotypes were identified. A hundred of 10 mer primers were used to amplified DNA from three pairs of NILs differing in the recessive branching gene "b". Few RAPD markers were identified by polymorphisms analysis and three RAPD markers D7-1800 bp, C1-750 bp and C1-1450 bp, are presented, but none of them discriminated consistently between branched and unbranched inbred lines in all three NILs, as we expected. For practical breeding work it is desirable to identify only positive markers associated with branched genotype.