Various ecomorphs of shallow-water Cisco Coregonus artedi were the dominant fish planktivores in each of the Great Lakes until invasive species and over fishing resulted in extirpations and extinctions. In this paper we describe the present morphological diversity and distribution of shallow-water Ciscoes in each of Lake Huron’s three basins: the main basin, Georgian Bay, and North Channel. Typical artedi, a formerly widespread ecomorph, which had supported the lake’s largest fishery, appears to have been extirpated from all three basins. Three types of shorthead ciscoes, a recently described and variable ecomorph, were extant. One type was morphologically robust and abundant along the north rim of the lake. The second type was large bodied, terete, short finned, and collected at only one location in the main basin. The third type consisted of putative shorthead cisco × typical artedi hybrids, which were widespread in Georgian Bay and the North Channel. Only the putative hybrids were regularly collected in midwater trawls, suggesting they were more-pelagic, which we attribute to an inferred partial ancestry with typical artedi. The putative shorthead cisco × typical artedi hybrids of Georgian Bay and the North Channel have replaced typical artedi to some degree, while shorthead ciscoes in the main basin, though possibly more abundant now than in the past, have not measurably replaced typical artedi. Even with the apparent extirpation of typical artedi, Lake Huron has a greater diversity of shallow-water Ciscoes than any of the other Great Lakes, which we attribute to its more-complex topography.