| Rank | City | 2009 Population (Est.) | Growth Rate (Annual) |
|---|---|---|---|
| 1 | Sioux Falls | 155,084 | 2.7% |
| 2 | Rapid City | 65,899 | 1.2% |
| 3 | Aberdeen | 24,881 | -0.2% |
| 4 | Watertown | 20,424 | 0.1% |
| 5 | Brookings | 19,965 | 0.7% |
| 6 | Mitchell | 14,725 | 0.1% |
| 7 | Pierre | 13,928 | 0.0% |
| 8 | Yankton | 13,807 | 0.3% |
| 9 | Huron | 11,072 | -0.9% |
| 10 | Vermillion | 10,485 | 0.3% |
| 11 | Spearfish | 9,928 | 1.7% |
| 12 | Brandon | 7,892 | 3.9% |
| 13 | Madison | 6,557 | 0.1% |
| 14 | Sturgis | 5,975 | -1.0% |
| 15 | Belle Fourche | 4,993 | 0.5% |
| 16 | Harrisburg | 4,869 | 22.1% |
| 17 | Tea | 4,344 | 11.7% |
| 18 | Canton | 4,221 | 3.8% |
| 19 | Box Elder | 4,063 | 2.1% |
| 20 | Hot Springs | 4,055 | -0.3% |
| 21 | Milbank | 3,201 | -1.6% |
| 22 | Mobridge | 3,157 | -1.5% |
| 23 | Dell Rapids | 3,117 | 0.5% |
| 24 | Lead | 2,870 | -0.6% |
| 25 | Lennox | 2,811 | 4.0% |
| 26 | Winner | 2,702 | -1.8% |
| 27 | North Sioux City | 2,542 | 1.3% |
| 28 | Sisseton | 2,468 | -0.4% |
| 29 | Chamberlain | 2,261 | -0.5% |
| 30 | Redfield | 2,236 | -1.5% |
| 31 | Flandreau | 2,233 | -0.8% |
| 32 | Beresford | 2,230 | 1.4% |
| 33 | Hartford | 2,205 | 2.0% |
| 34 | Fort Pierre | 2,078 | 0.2% |
| 35 | Custer | 1,997 | 0.2% |
| 36 | Elk Point | 1,945 | 1.6% |
| 37 | Webster | 1,668 | -1.9% |
| 38 | Volga | 1,602 | 1.2% |
| 39 | Wagner | 1,498 | -0.9% |
| 40 | Springfield | 1,477 | -0.7% |
| 41 | Parkston | 1,474 | -1.5% |
| 42 | Groton | 1,403 | 0.5% |
| 43 | Miller | 1,334 | -1.7% |
| 44 | Salem | 1,314 | -0.7% |
| 45 | Platte | 1,284 | -0.7% |
| 46 | Deadwood | 1,274 | -0.9% |
| 47 | Britton | 1,235 | -0.9% |
| 48 | Clear Lake | 1,211 | -1.2% |
| 49 | Mission | 1,210 | 3.7% |
| 50 | Freeman | 1,182 | -1.3% |
| 51 | Lemmon | 1,182 | -2.0% |
| 52 | Gregory | 1,169 | -2.2% |
| 53 | Worthing | 1,153 | 8.5% |
| 54 | Crooks | 1,099 | 3.0% |
| 55 | Garretson | 1,095 | -0.8% |
| 56 | Tyndall | 1,089 | -1.6% |
| 57 | De Smet | 1,073 | -1.4% |
| 58 | Clark | 1,072 | -2.2% |
| 59 | Gettysburg | 1,048 | -3.0% |
| 60 | Martin | 986 | -1.1% |
| 61 | Parker | 976 | -0.8% |
| 62 | Eureka | 941 | -1.9% |
| 63 | Eagle Butte | 924 | 0.2% |
| 64 | Arlington | 919 | -1.0% |
| 65 | Hill City | 915 | 2.0% |
| 66 | Baltic | 910 | 1.3% |
| 67 | Alcester | 895 | 0.2% |
| 68 | Howard | 877 | -2.5% |
| 69 | Ipswich | 852 | -1.2% |
| 70 | Whitewood | 851 | 0.1% |
| 71 | Centerville | 839 | -1.0% |
| 72 | Wessington Springs | 836 | -2.3% |
| 73 | Marion | 820 | -1.0% |
| 74 | Wall | 811 | -0.1% |
| 75 | Edgemont | 782 | -1.2% |
| 76 | Scotland | 781 | -1.6% |
| 77 | Valley Springs | 777 | -0.3% |
| 78 | Viborg | 770 | -1.0% |
| 79 | St. Francis | 761 | 1.0% |
| 80 | Lake Andes | 756 | -1.0% |
| 81 | McLaughlin | 728 | -0.7% |
| 82 | Philip | 718 | -2.5% |
| 83 | Highmore | 699 | -2.4% |
| 84 | Kimball | 692 | -0.9% |
| 85 | New Underwood | 682 | 1.1% |
| 86 | Castlewood | 676 | 0.2% |
| 87 | Faulkton | 672 | -1.9% |
| 88 | Estelline | 665 | -0.2% |
| 89 | Armour | 660 | -2.0% |
| 90 | Canistota | 654 | -0.9% |
| 91 | Menno | 651 | -1.3% |
| 92 | Selby | 651 | -1.5% |
| 93 | Elkton | 648 | -0.5% |
| 94 | Alexandria | 646 | 1.7% |
| 95 | Lake Preston | 644 | -1.7% |
| 96 | Woonsocket | 640 | -1.4% |
| 97 | Newell | 628 | -0.4% |
| 98 | Tripp | 626 | -1.6% |
| 99 | Kadoka | 623 | -1.6% |
| 100 | Presho | 623 | 0.6% |
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