Minecraft wiki entry for Nether_portals, associated text: The Y coordinate is not divided for pairings, however it does play a factor in mapping the portals. Therefore, two Overworld portals could be built at the same x,z coordinates with one at a very low Y, e.g., 5, and one at a higher y, e.g. 160. A Nether portal at these X and Z coordinates will link to whichever portal is closest on the Y axis.