The emergence of reproductive isolation is key in maintaining within- and between-species diversity and one of the initial steps of speciation. In the Iberian Peninsula, the diverging populations of the Brachionus plicatilis rotifer create an ideal system to shed light on the mechanisms that give rise to the emergence of reproductive isolation. Herein, we quantify the degree of behavioural reproductive isolation in two groups of B. plicatilis populations, namely, neighbouring populations diverging by adaptation to the local environment and populations diverging in the absence of gene flow due to geographic distance. We conduct behavioural no-choice assays to test mating reproductive isolation between these populations. The analysis shows signatures of ongoing behavioural reproductive isolation in most of the population crosses, which is more pronounced in populations with a higher level of adaptive divergence, presumably under high migration rates. Overall, this study suggests that local adaptation is associated with mating behaviour resulting in reproductive isolation.