A semiconductor device includes a first stack structure on a substrate, and a second stack structure on the first stack structure. A channel structure extends through the first stack structure and the second stack structure. A first auxiliary stack structure including a plurality of first insulating layers and a plurality of first mold layers are alternately stacked on the substrate. An alignment key extends into the first auxiliary stack structure and protrudes to a higher level than an uppermost end of the first stack structure. A second auxiliary stack structure is disposed on the first auxiliary stack structure and the alignment key, and includes a plurality of second insulating layers and a plurality of second mold layers alternately stacked. The second auxiliary stack structure includes a protrusion aligned with the alignment key.