Cisco (Coregonus artedi) are a native fish that were historically abundant and a prominent component of Great Lakes ecosystems. However, widespread declines involving the loss of some spawning populations occurred, primarily due to overfishing. This thesis presents observations of diverse spawning habitat preferences among three extant Cisco populations based on the distribution of incubating eggs across depth and substrate gradients. Cisco in Chaumont Bay, Lake Ontario were confirmed to target shallow bedrock shoals for spawning, whereas those in Thunder Bay, Lake Superior and Grand Traverse Bay, Lake Michigan appear to spawn in deeper waters over soft sediment. Evaluations of the diaphragm pump used to sample eggs in the field and the efficacy of using egg size to distinguish Cisco eggs from other species supported this work. The results presented here contribute new information about existing population diversity in support of management decisions targeting Cisco rehabilitation in the Great Lakes.