The mechanisms that maintain isolation between divergent forms (species and sub-species) that are found in ecological contact with one another can provide important insight into the process of speciation and also the maintenance of variation in a variety of traits relating to reproduction. The two sub-species of the long-tailed finch (Poephila acuticauda) provide a very good opportunity for such work because they can be readily held and bred experimentally in captivity. The long-tailed finch is currently classified into two subspecies: P. a. acuticauda (yellow-billed) and P. a. hecki (red-billed). Despite a narrow zone of secondary contact, these subspecies are maintained as these two distinct forms. The mechanism for the maintenance of these two forms is unknown. Despite significant differences in sperm morphology, heterosubspecific matings produce viable orange-billed offspring. In this study, we experimentally tested pair compatibility and its potential mechanisms by combining long-tailed finch pairs assortatively or dissassortatively with respect to bill colour form (red, yellow, or hybrid orange). We assessed the effect of pair compatibility on adult physiology by quantifying post-copulatory investment and outcome by measuring stress levels (through corticosterone levels) in plasma and egg yolks, and the number of sperm that reached the ova across two clutches of eggs. Consistent with our hypothesis, we found that more sperm reached the ova and are trapped on the perivitelline membrane in assortative pairs; improving the chance of fertlisation. We suggest this difference in sperm numbers in the egg is due in part because of observable differences in sperm morphology between the sub-species, but is also impacted by the stress on adults in experimentally enforced dissassortative pairing.  These findings have implications for understanding the evolution of reproductive isolation and the evolution of genetic polyandry in animals.