In Japan, rice paddies have acted as a substitute habitat for pond-breeding frogs. However, since the 1950s, agricultural modernization has altered the rice paddy environment, and pond-breeding frog populations have been decreasing. This agricultural modernization has led to rice paddy fragmentation via roadways and the construction of deep channels. To assess the influences of habitat fragmentation, we compared the distribution of two pond-breeding frogs, a common species, Hyla japonica, and an endangered species, Pelophylax porosa brevipoda, around a deep roadside ditch. In Shiga prefecture, we selected two rice paddies along a roadway and recorded the number of frogs and their snout-vent length (SVL) at the levee of a rice paddy, ditch, bank, and adjacent roadway. In total, we identified 1,293 P. p. brevipoda and 181 H. japonica. Most P. p. brevipoda were either at the levee or ditch, and the number of this species found in the ditch was much higher than in any other location in July and October. The SVLs of P. p. brevipoda found in the ditch in June were smaller than those in October. Most H. japonica were at the levee or bank, and there were no apparent temporal or spatial patterns of distribution. Our results suggest that the ditch acts as a barrier to juveniles in early summer and to all frogs during autumn for P. p. brevipoda but not for H. japonica. For long-term conservation, it is important to study the movement patterns related to life history and rice paddy management.