| Rank | City | 2000 Population |
|---|---|---|
| 1 | Magdalena | 910 |
| 2 | Cloudcroft | 763 |
| 3 | Melrose | 734 |
| 4 | Vaughn | 539 |
| 5 | Reserve | 389 |
| 6 | Jemez Springs | 372 |
| 7 | Wagon Mound | 371 |
| 8 | Roy | 299 |
| 9 | San Jon | 278 |
| 10 | Willard | 261 |
| 11 | Mosquero | 119 |
| 12 | Folsom | 75 |
| 13 | Deming | 14,305 |
| 14 | Espanola | 9,700 |
| 15 | Tucumcari | 5,941 |
| 16 | Santa Fe | 63,286 |
| 17 | Lordsburg | 3,277 |
| 18 | Rio Rancho | 52,706 |
| 19 | Ruidoso Downs | 2,650 |
| 20 | Mesilla | 2,492 |
| 21 | Edgewood | 1,985 |
| 22 | Santa Clara | 1,938 |
| 23 | Milan | 1,899 |
| 24 | Questa | 1,868 |
| 25 | Columbus | 1,755 |
| 26 | Hurley | 1,458 |
| 27 | Tatum | 706 |
| 28 | Springer | 1,285 |
| 29 | Alamogordo | 35,166 |
| 30 | Cuba | 593 |
| 31 | Dexter | 1,244 |
| 32 | Fort Sumner | 1,231 |
| 33 | Chama | 1,204 |
| 34 | Mountainair | 1,119 |
| 35 | Clovis | 32,566 |
| 36 | Logan | 1,097 |
| 37 | Grenville | 25 |
| 38 | Williamsburg | 526 |
| 39 | Tijeras | 497 |
| 40 | Red River | 485 |
| 41 | Lake Arthur | 431 |
| 42 | Eagle Nest | 305 |
| 43 | Maxwell | 274 |
| 44 | San Ysidro | 236 |
| 45 | Elida | 182 |
| 46 | Des Moines | 176 |
| 47 | Corona | 165 |
| 48 | Virden | 139 |
| 49 | Dora | 130 |
| 50 | Floyd | 78 |
| 51 | Hope | 107 |
| 52 | Grady | 98 |
| 53 | Encino | 94 |
| 54 | House | 71 |
| 55 | Causey | 61 |
| 56 | Taos Ski Valley | 56 |
| 57 | Las Vegas | 14,565 |
| 58 | Sunland Park | 13,385 |
| 59 | Portales | 11,132 |
| 60 | Artesia | 10,753 |
| 61 | Silver City | 10,497 |
| 62 | Los Lunas | 10,115 |
| 63 | Lovington | 9,522 |
| 64 | Socorro | 8,862 |
| 65 | Grants | 8,818 |
| 66 | Ruidoso | 7,985 |
| 67 | Truth or Consequences | 7,290 |
| 68 | Raton | 7,270 |
| 69 | Corrales | 7,267 |
| 70 | Belen | 7,180 |
| 71 | Bloomfield | 6,734 |
| 72 | Bernalillo | 6,582 |
| 73 | Aztec | 6,495 |
| 74 | Los Ranchos de Albuquerque | 5,436 |
| 75 | Taos | 4,750 |
| 76 | Bosque Farms | 3,942 |
| 77 | Peralta | 3,535 |
| 78 | Tularosa | 2,989 |
| 79 | Santa Rosa | 2,755 |
| 80 | Eunice | 2,576 |
| 81 | Bayard | 2,525 |
| 82 | Clayton | 2,517 |
| 83 | Jal | 2,005 |
| 84 | Moriarty | 1,866 |
| 85 | Hobbs | 28,612 |
| 86 | Carlsbad | 25,605 |
| 87 | Gallup | 20,805 |
| 88 | Hatch | 1,636 |
| 89 | Estancia | 1,585 |
| 90 | Capitan | 1,456 |
| 91 | Pecos | 1,441 |
| 92 | Elephant Butte | 1,402 |
| 93 | Loving | 1,339 |
| 94 | Hagerman | 1,167 |
| 95 | Texico | 1,062 |
| 96 | Angel Fire | 1,058 |
| 97 | Carrizozo | 1,035 |
| 98 | Cimarron | 918 |
| 99 | Albuquerque | 450,557 |
| 100 | Las Cruces | 73,605 |
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