An encoder includes circuitry and memory coupled to the circuitry. The circuitry: assigns a picture level slice index and a subpicture level slice index to each of the slices, the picture level slice index being assigned at a picture level, the subpicture level slice index being assigned at a subpicture level; for each of the slices, encodes the subpicture level slice index of the slice into a slice header of the slice; and encodes each of the slices into a bitstream. The picture level slice index assigned to a current slice to be processed that is included in a current subpicture to be processed is calculated by adding (i) the subpicture level slice index of the current slice and (ii) a total number of slices included in one or more subpictures that have been encoded prior to the current subpicture out of the subpictures.