The productivity of many tree crops is limited by low yield, partly due to high rates of fruitlet abscission during early fruit development. Early studies suggested that cross-pollinated fruitlets may be selectively retained during fruit development, although paternity testing of fruitlets to test this hypothesis was technically challenging. We used MassARRAY genotyping to determine the effects of pollen parentage on fruitlet retention and fruit quality of Hass avocado. We identified the paternity of abscised and retained fruitlets at 6 and 10 weeks, and mature fruit at 36 weeks, after peak anthesis. We measured the embryo mass, pericarp mass, total mass and nutrient concentrations of fruitlets, and the seed mass, flesh mass, total mass, diameter, length, nutrient concentrations and fatty-acid composition of mature fruit. The percentages of progeny on the tree that were cross-fertilised increased from 4.6% at 6 weeks after peak anthesis to 10.7% at fruit maturity. Only 1.0% of freshly abscised fruitlets on the ground at 10 weeks after peak anthesis were cross-pollinated even though 6.5% of retained fruitlets on the tree were cross-pollinated. At this stage, cross-pollinated fruitlets had similar nutrient concentrations to self-pollinated fruitlets, but they had higher total contents of P, K, Al, Ca, Fe, Mn and Zn due to having greater fruitlet mass. At maturity, cross-pollinated fruit were 6% heavier and had 2% greater diameter than self-pollinated fruit, without significant differences in flesh nutrient concentrations or fatty acid composition. The results demonstrate that Hass avocado trees selectively retain cross-pollinated fruitlets, which are larger than self-pollinated fruitlets and ultimately produce larger mature fruit. Avocado growers can increase fruit size and yield by improving the opportunities for cross-pollination, possibly by closely interplanting type A and type B cultivars and introducing more beehives into orchards.