Speciation is nowadays recognized as a dynamic process in which the respective roles of forces driving ecological differentiation and reproductive isolation can change through time and space. Incipient speciation events are particularly useful to follow such processes that are not tractable when considering well-differentiated taxa. A promising case study was discovered in the pine processionary moth, Thaumetopoea pityocampa, a Mediterranean defoliator of Pinus species, for which allochrony acting as an automatic magic trait was recognized as the major driver of an incipient speciation process. In Portugal, a unique population with a shifted phenology, known as the summer population (SP), co-occurs with a population following the typical life cycle, known as the winter population (WP). We monitored male activity of both populations in the Leiria region, i.e. over the whole SP distribution range using a systematic sampling along two transects, and studied Portuguese WPs at a larger geographical scale to explore their genetic diversity and spatial pattern of differentiation. Results showed that the WPs were genetically more diverse than the SP, with a strong pattern of isolation by distance both at large and small spatial scales, while the SP was very homogeneous over its whole range, without signature of its recent spatial expansion. Contrary to our expectations, no F1 hybrids were identified, even though we found an extended flight period of the SP, overlapping with the beginning of the WP reproductive period. Interestingly, the SP was found to be mostly limited to the sea shore where the WP is now scarce or absent, which could suggest competitive exclusion. Once clearly occurring in a sympatric context, the allochronic differentiation tends to develop nowadays in parapatry.