The maintenance of reproductive isolation in the face of gene-flow is a particularly contentious topic, but differences in reproductive behaviour may provide the key to explaining this phenomenon. However, we do not yet fully understand how behaviour contributes to maintaining species boundaries. How important are behavioural differences during reproduction? To what extent does assortative mating maintain reproductive isolation in recently diverged populations and how important are ‘magic traits’? Assortative mating can arise as a by-product of accumulated differences between divergent populations as well as an adaptive response to contact between those populations, but this is often overlooked. Here we address these questions using recently described species-pairs of three-spined stickleback (Gasterosteus aculeatus), from two separate locations and a phenotypically intermediate allopatric population on the island of North Uist, Scottish Western Isles. We identified stark differences in the preferred nesting substrate, and courtship behaviour of species-pair males. We showed that all males selectively court females of their own ecotype and all females prefer males of the same ecotype, regardless of whether they are from species-pairs or allopatric populations. We also showed that mate choice does not appear to be driven by body-size differences (a potential ‘magic trait’). By explicitly comparing the strength of these mating preferences between species-pairs and single-ecotype locations we were able to show that present levels of assortative mating due to direct mate choice are likely a by-product of other adaptations between ecotypes, and not subject to obvious selection in species-pairs. Our results suggest that ecological divergence in mating characteristics, particularly nesting microhabitat may be more important than direct mate choice in maintaining reproductive isolation in stickleback species-pairs.