Breeding programs for horticultural tree crops focus on enhancing productivity, including developing tolerance to pests and diseases and improving crop quality. Pollination services are often critical for crop production, and pollen parents can affect crop quality. We often do not know which pollen parents produce highest quality offspring or, in self-compatible cultivars, how much of the crop comes from cross- versus self-pollination. We quantified the proportions of self- and cross-paternity in an open pollination setting of five standard commercial almond cultivars and of six new almond cultivars selected for yield, kernel size, taste or self-compatibility. We assessed how pollination by different parents affected kernel size and nutritional quality. Kernels from most commercial cultivars and from the new cultivars selected for taste and size resulted almost entirely from cross-pollination. Most kernels from the commercial cultivar ‘Price’ resulted from cross-pollination but 21% resulted from self-pollination. In contrast, 48–91% of kernels from the new self-compatible cultivars resulted from self-pollination. Different cross-pollen parents did not greatly affect kernel size or quality. The proportions of self-paternity in the new self-compatible cultivars varied strongly in an open pollination setting suggesting that some cultivars may be good candidates for establishing monovarietal orchards.