Most primates use diagonal sequence (DS), diagonal couplets (DC) gaits when they walk or run quadrupedally, and it has been suggested that DSDC gaits contribute to stability in their natural arboreal habitats compared to other symmetrical gaits. However, this postulate is based solely on studies of primate gaits using continuous terrestrial and arboreal substrates. A particular species may select suitable gaits according to the substrate properties. Here, we analyzed the gaits of Japanese macaques moving on a horizontal ladder with rung intervals ranging from 0.40 to 0.80 m to elucidate the relative advantages of each observed form of gait. The rung arrangement forced our macaques to choose either diagonal coupling or DS gaits. One macaque consistently used diagonal coupling (i.e., DSDC and LSDC gaits) across narrow and intermediate rung intervals, whereas the other macaque used DS gaits (i.e., DSDC and DSLC gaits). At wider rung intervals, both macaques shifted to a two-one sequence (TOS), which is characterized by two nearly simultaneous touchdowns of both forelimbs and one touchdown of each hind limb in a stride. The transition to the TOS sequence increased the duration of support on multiple limbs, but always included periods of a whole-body aerial phase. These results suggest that Japanese macaques prefer DSDC gaits, because the diagonal coupling and DS contribute separately to stability on complex supports compared to the lateral coupling and lateral sequence. We also postulate that stability triggers the transition from symmetrical gaits to the TOS sequence.