Pollen limitation occurs when insufficient pollen or the wrong pollen genotype reaches the stigma, resulting in failure to fertilise ovules and trigger seed development. The pollination efficiency of flower visitors to crops has been investigated previously, assessing their on-flower behaviour or amount of pollen deposited during a single flower visit. However, the genotypes of crop pollen carried by flower visitors have rarely been identified even though many crops depend on, or benefit from, cross-pollination for seed production. Here, we developed a genotyping method that can detect both high-abundance and low-abundance single nucleotide polymorphisms (SNPs) in the DNA of pollen carried by a single bee. This method uses a customised single allele base extension reaction (SABER) with MassARRAY detection to distinguish genotypes that contribute only a small fraction to a mixed-genotype pollen sample. We used this method to identify the cultivars of pollen carried by honeybees at increasing distances from a cross-pollen source. We assessed the percentage of honeybees that carried cross-pollen in two different multi-cultivar macadamia orchards, one where each single-cultivar block was 5 rows wide and another where each single-cultivar block was more than 40 rows wide. This percentage of honeybees represents the maximum that potentially contribute to cross-pollination and seed production in self-incompatible crops, such as macadamia. Many honeybees carried exclusively self-pollen, with only 30–53 % of honeybees carrying cross-pollen. Distance from a cross-pollen source did not significantly affect the percentage of honeybees carrying cross-pollen in either orchard. This study demonstrates significant potential to increase the effectiveness of honeybees as pollinators. Orchards can be re-designed to interplant cross-pollen sources and maximise the number of honeybees contributing to crop production. Improving pollination effectiveness will help to alleviate the growing shortfall in the supply of beehives required for crop pollination.