Behavioural isolating mechanisms involving male advertisement calls and female phonotaxis may be unreliable when closely-related sympatric species interact with each other in close proximity, and when these two species exhibit incomplete pre- and post-mating reproductive isolation. Then, other mechanisms such as temporal and/or spatial differentiation of microhabitat use may evolve. Two treefrog species co-occur in Korea: the endangered Hyla suweonensis and the widespread H. japonica. Advertisement calls are differentiated between these two species, but whether call differences are sufficient for reproductive isolation is unclear. We tested the possibility of fine-scale differentiation in microhabitat use for an added mechanism of reproductive isolation between the two species, based on call monitoring within rice paddies and individual tracking during the breeding period. Both treefrog species showed similar patterns of microhabitat use in their diel cycle and occurred in all five microhabitats: rice paddy, ground, buried, grass, and bush. However, males H. suweonensis moved into rice paddies and produced advertisement calls three hours ahead of males H. japonica.Furthermore, H. suweonensis called from the centre of rice paddies while “holding”, whereas H. japonica called from the edges, while “sitting” onto the substrate. Males H. suweonensis rested in bushes in the morning but left an hour before males H. japonica arrived. Individual movement patterns revealed spatial and temporal differentiations in microhabitat use for calling and resting during the breeding season. Such patterns are likely to minimize contacts during daily movements and create an effective premating barrier between the two species. We suggest that the role of calling site selection may be underestimated for reproductive isolation in multi-species anuran communities and that spatial differentiation may complement the differences in acoustic communication for reproductive isolation.