The modern nursery industry requires seed sources of a high quality and regular quantity year by year. Besides the seed sources of processed cultivars (Bartlett pear, Shipley, Elberta peach) special seed orchards are planted with selected seed trees producing high quality and genetically determined seed (hybrid seed or inbred lines). Seedlings are still the most common commercial source of rootstocks for stone fruits (almond, apricot, peach, plum, prune and walnut). Although clonal rootstocks are spreading, usage of seedlings is still predominant at stone fruits and nuts. For successful seed production and planning of seed orchard the knowledge on floral biology, flower fertility, pollination, blossom time of trees (selected clone or cultivars) used for seed production is essential. In this field very little systematic research was carried out most of the papers were published in the second half of the 20th century. Our mini review gives an overview on the importance of flower fertility in the mating systems applied in seed orchards, and the research results on floral biology of fruit tree rootstocks propagated by seed (Prunus avium, Prunus mahaleb, Prunus armeniaca, Prunus cerasifera, Prunus insititia, Prunus amygdalus, P persica, P amygdalopersica, Pyrus pyraster, Pyrus communis and Pyrus betulifolia) over the last decades.