| Rank | City | 2006 Population (Est.) | Growth Rate (Annual) |
|---|---|---|---|
| 1 | Sioux Falls | 145,095 | 2.9% |
| 2 | Rapid City | 62,373 | 0.8% |
| 3 | Aberdeen | 24,762 | -0.3% |
| 4 | Watertown | 20,161 | -0.1% |
| 5 | Brookings | 18,860 | 0.0% |
| 6 | Mitchell | 14,734 | 0.2% |
| 7 | Pierre | 13,967 | 0.1% |
| 8 | Yankton | 13,654 | 0.2% |
| 9 | Huron | 10,984 | -1.5% |
| 10 | Vermillion | 10,169 | -0.2% |
| 11 | Spearfish | 9,526 | 1.9% |
| 12 | Brandon | 6,700 | 2.9% |
| 13 | Sturgis | 6,275 | -0.6% |
| 14 | Madison | 6,215 | -1.0% |
| 15 | Belle Fourche | 4,825 | 0.0% |
| 16 | Hot Springs | 4,086 | -0.3% |
| 17 | Canton | 3,863 | 4.2% |
| 18 | Box Elder | 3,548 | 0.7% |
| 19 | Milbank | 3,312 | -1.8% |
| 20 | Mobridge | 3,259 | -1.7% |
| 21 | Tea | 3,025 | 11.0% |
| 22 | Dell Rapids | 2,979 | -0.1% |
| 23 | Lead | 2,918 | -0.7% |
| 24 | Winner | 2,896 | -1.5% |
| 25 | Lennox | 2,558 | 4.5% |
| 26 | Sisseton | 2,479 | -0.5% |
| 27 | North Sioux City | 2,476 | 1.6% |
| 28 | Redfield | 2,309 | -1.8% |
| 29 | Harrisburg | 2,308 | 18.5% |
| 30 | Flandreau | 2,280 | -0.8% |
| 31 | Chamberlain | 2,238 | -0.9% |
| 32 | Beresford | 2,095 | 0.9% |
| 33 | Fort Pierre | 2,061 | 0.2% |
| 34 | Custer | 2,002 | 0.3% |
| 35 | Hartford | 1,927 | 0.4% |
| 36 | Elk Point | 1,818 | 1.1% |
| 37 | Webster | 1,762 | -1.9% |
| 38 | Parkston | 1,538 | -1.6% |
| 39 | Wagner | 1,525 | -1.1% |
| 40 | Springfield | 1,505 | -0.7% |
| 41 | Volga | 1,497 | 0.5% |
| 42 | Groton | 1,371 | 0.3% |
| 43 | Salem | 1,365 | -0.4% |
| 44 | Miller | 1,361 | -2.4% |
| 45 | Deadwood | 1,309 | -1.0% |
| 46 | Platte | 1,301 | -0.9% |
| 47 | Britton | 1,263 | -1.0% |
| 48 | Clear Lake | 1,234 | -1.5% |
| 49 | Gregory | 1,227 | -2.5% |
| 50 | Freeman | 1,208 | -1.7% |
| 51 | Lemmon | 1,203 | -2.8% |
| 52 | Gettysburg | 1,151 | -2.9% |
| 53 | Clark | 1,145 | -2.2% |
| 54 | Tyndall | 1,132 | -1.7% |
| 55 | De Smet | 1,109 | -1.6% |
| 56 | Garretson | 1,080 | -1.6% |
| 57 | Martin | 1,024 | -1.0% |
| 58 | Crooks | 1,001 | 2.9% |
| 59 | Eureka | 989 | -2.1% |
| 60 | Parker | 987 | -1.1% |
| 61 | Mission | 944 | 0.8% |
| 62 | Eagle Butte | 942 | 0.7% |
| 63 | Arlington | 934 | -1.2% |
| 64 | Howard | 927 | -2.8% |
| 65 | Worthing | 921 | 8.9% |
| 66 | Wessington Springs | 899 | -2.2% |
| 67 | Alcester | 880 | 0.0% |
| 68 | Ipswich | 878 | -1.4% |
| 69 | Baltic | 869 | 1.1% |
| 70 | Centerville | 852 | -1.3% |
| 71 | Hill City | 848 | 1.6% |
| 72 | Whitewood | 840 | -0.1% |
| 73 | Marion | 822 | -1.6% |
| 74 | Edgemont | 814 | -1.1% |
| 75 | Scotland | 814 | -1.7% |
| 76 | Wall | 810 | -0.2% |
| 77 | Highmore | 790 | -1.4% |
| 78 | Viborg | 788 | -1.1% |
| 79 | Lake Andes | 773 | -1.1% |
| 80 | St. Francis | 760 | 1.5% |
| 81 | Philip | 758 | -2.9% |
| 82 | Valley Springs | 754 | -1.1% |
| 83 | McLaughlin | 752 | -0.4% |
| 84 | Armour | 716 | -1.6% |
| 85 | Faulkton | 686 | -2.6% |
| 86 | Canistota | 686 | -0.5% |
| 87 | Menno | 684 | -1.1% |
| 88 | Kimball | 682 | -1.7% |
| 89 | Selby | 677 | -1.6% |
| 90 | Estelline | 669 | -0.3% |
| 91 | Lake Preston | 667 | -2.0% |
| 92 | Woonsocket | 666 | -1.5% |
| 93 | Castlewood | 664 | -0.1% |
| 94 | New Underwood | 661 | 1.2% |
| 95 | Tripp | 659 | -1.5% |
| 96 | Alexandria | 657 | 3.0% |
| 97 | Kadoka | 653 | -1.6% |
| 98 | Onida | 645 | -2.6% |
| 99 | Elkton | 639 | -1.1% |
| 100 | Newell | 632 | -0.5% |
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