Malaria parasites are obligately sexual hermaphrodite protozoans, with gamete fusion occurring in the mosquito midgut, followed by meiosis and recombination. Fusion of male and female gametes of the same genotype results in self-fertilization (\"selfing\"), while \"outcrossing\" occurs between gametes of different parasite genotypes. Previous work has used PCR-based methods to assess oocyst genotypes in laboratory crosses and natural mosquito infections, revealing either random mating or inbreeding, but this approach is labor intensive and prone to technical issues. We generated florescent-labelled clones of NF54 (mCherry), an African parasite, and NHP4026 (GFP), a Thai parasite, crossed these parasites, and scored genotypes of 8540 oocysts from 435 mosquitoes sampled from 7 to 14 days post infection. We observed decreasing proportions of outcrossed oocysts and increasing levels of inbreeding over the course of the infection in two independently replicated crosses. These results are consistent with the faster maturation of transmissible sporozoites derived from outcrossed compared with selfed oocysts. We also found that selfed NF54 oocysts were larger than outcrossed and selfed NHP4026 oocysts. Our results reveal outcrossing advantages, perhaps due to outcrossing allowing for the removal of deleterious mutations accumulated during asexual parasite replication in the vertebrate host. Oocyst genotype significantly impacts oocyst size which may influence production of sporozoites and onward transmission. Overall, fluorescent labelling provides clear resolution of mating patterns, temporal dynamics and transmission potential of malaria parasites in mosquitoes. Importantly, faster maturation of outcrossed parasites can maximize levels of recombination in transmitted malaria parasite populations.