The alphamegalog of the cities of South Dakota lists the largest city in South Dakota for each letter of the alphabet. In this case, ‘largest’ is based on population within the city proper.

Aberdeen
Brookings
Canton
Dell Rapids
Elk Point
Flandreau
Groton
Huron
Ipswitch
Johnson Siding
Kyle
Lead
Mitchell
North Souix City
Oglala
Pierre
(no Q)
Rapid City
Souix Falls
Tea
Upland Colony
Vermillion
Watertown
(no X)
Yankton
(no Z)