To perceive multiple overlapping surfaces in the same location of the visual field (transparency), the visual system must determine which surface elements belong together, and should be integrated, and which should be kept apart. Spatial relations between surfaces, such as depth order, must also be determined. This article details two experiments examining the interaction of motion direction and disparity cues on the perception of depth order and surface segmentation in transparency. In Experiment 1, participants were presented with random-dot stereograms, where transparent planes were defined by differences in motion direction and disparity. Participants reported the direction of motion of the front surface. Results revealed marked effects of motion direction on perceived depth order. These biases interact with disparity in an additive manner, suggesting that the visual system integrates motion direction with other available cues to surface segmentation. This possibility was tested further in Experiment 2. Participants were presented with two intervals: one containing motion and disparity defined transparent planes, the other containing a volume of moving dots. Interplane disparity was varied to find thresholds for the correct identification of the transparent interval. Thresholds depended on motion direction: Thresholds were lower when disparities and directions in the transparency interval matched participants' preferred depth order, compared to conditions where disparity and direction were in conflict. These results suggest that motion direction influences the judgment of depth order even in the presence of other visual cues, and that the assignment of depth order may play an important role in segmentation.