Vertical phoria (vergence error under monocular viewing conditions) can be trained to vary with conjugate eye position. The adaptive response controls the vertical alignment of the two eyes in the absence of binocular disparity and is used to compensate for binocular changes of the oculomotor system induced by developmental and environmental factors. Vertical phoria was associated with horizontal disparity vergence by adapting vertical vergence to two vertically disparate targets separated along the depth axis. This association was primarily dependent on the horizontal vergence as opposed to monocular eye position or binocular conjugate eye position. Following this adapted association with horizontal disparity vergence, vertical phoria aftereffects were also evoked by accomodative vergence. Previous reports have demonstrated an adapted association between vertical phoria and conjugate eye position. The current report examines the difference in the vertical phoria resulting from adaptation to vertically disparate targets separated along either the vertical axis or depth axis. The amplitude of the vertical vergence aftereffect was approximately 4 times greater for targets separated along the depth axis than in the vertical meridian. The association between vertical phoria with conjugate eye position and horizontal vergence is proposed to result from a cross-coupling of vertical vergence with supranuclear regions that control conjugate and horizontal vergence eye movements. A selective interaction would enable the oculomotor system to correct disturbances in specific supranuclear regions as they interface with vertical vergence.