A 3D semiconductor device, the device including: a first level including a first single crystal layer, the first level including first transistors, where each of the first transistors includes a single crystal channel; first metal layers interconnecting at least the first transistors; a second metal layer overlaying the first metal layers; a first oxide layer disposed over the second metal layer; a second oxide layer disposed over the first oxide layer; and a second level including at least one array of memory cells and second transistors, where each of the memory cells includes at least one of the second transistors, where the second level overlays the first level, where at least one of the second transistors includes at least two independent gates, where the second level is directly bonded to the first level, and where the bonded includes direct oxide-to-oxide bonds.