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In flowering plants, such as Hydrangea macrophylla, the main breeding objective is to increase genetic variability in ornamental traits. This study investigates in vitro techniques, through ovule culture, to overcome the hybridization barriers and increase the efficiency of crossing in Hydrangea macrophylla in which breeding has been hampered by a fairly long breeding cycle and lack of information about its genetic resources. Two different types of media were compared, Gamborg B5 and Murashige and Skoog basal salts, to verify the germination rate of immature ovules in different intraspecific crosses. The germination rate and viability of the seedlings were influenced by the parental genotypes in the different combinations of crossing, highlighting, in some cases, the poor compatibility between some of them. The crossing combination “Parental A × Parental B”, showed the highest germinated ovules percentage (78.3%). The media used seem to less affect the ovule germination while mainly influencing the development and growth of the young seedlings and in particular the number of leaves, the branching attitude, and root length, with the Gamborg medium determining up to a 30% increase, compared to MS medium. In addition, we tested the effectiveness of using SSR markers to assess the parentage of the putative hybrids even though only three out of twelve SSR markers showed allelism. Although the number of SSR markers was low, they were allowed to profile the parentage according to Mendelian laws.