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| Town | Township | Notes |
| Alma | Butler |
| America | Brandon |
| Amoy | | Was a P.O., not on county maps |
| Andrew | Perry | existing, former county seat |
| Baldwin | Monmouth | existing |
| Bellevue | Bellevue | existing |
| Bridgeport | Maquoketa | cemetery |
| Buckhorn | South Fork |
| Canton | Brandon | existing |
| Carrollport | Union | changed to Charleston about 1840 |
| Charleston | Union | changed to Sabula in 1846 |
| Clarkstown | Washington | changed to Green Island |
| Cobb | Monmouth | changed to Millrock |
| Coloma | Monmouth | now part of Monmouth |
| Copper Creek | Van Buren | changed to Van Buren |
| Cottonville | Richland | cemetary |
| Crabb's Mills | Brandon |
| Duggan | Butler |
| Duke | Prairie Springs |
| Emeline | Brandon | existing |
| Esgate | Farmer's Creek |
| Farmer's Creek | South Fork |
| Franklin | Monmouth |
| Fremont | Monmouth | now part of Baldwin |
| Fulton | Farmer's Creek | existing |
| Garryowen | Butler | existing, mainly church and cemetery |
| Gordon's Ferry | Tetes des Mort |
| Green Island | Washington | existing |
| Hickory Grove | Bellevue | cemetery in Brandon Township |
| Higginsport | Van Buren |
| Hugo | Butler |
| Hurstville | South Fork | ghost town |
| Iron Hill | Farmer's Creek | existing |
| Lainsville | | ghost town, former resort area |
| Lakehurst | South Fork |
| LaMotte | Richland, Pr. Springs | existing |
| Lowell | | north of Maquoketa |
| Maple Grove | Farmer's Creek |
| Maquoketa | Maquoketa, S. Fork | County Seat |
| Miles | Iowa, Van Buren | existing |
| Millrock | Monmouth | school still there |
| Monmouth | Monmouth | existing |
| Mount Algor | Van Buren |
| Nashville | South Fork | existing, nicknamed "Pumpkin Center" |
| New Castle | Farmer's Creek | school named this |
| North Bellevue | Bellevue |
| North Maquoketa | | may be same as Lowell or Springfield |
| Oak Grove | Brandon | existing |
| Otter Creek | Otter Creek | also known as Burns Settlement |
| Ozark | Brandon | may be a school there |
| Preston | Van Buren | existing |
| Rolley | Fairfield |
| Sabula | Union | existing |
| Sabula Junction |
| Saint Donatus | Tetes des Mort | existing |
| Silsbee | Perry | changed to Andrew 1841 |
| Smith's Ferry |
| South Garryowen | Butler | church may still be there |
| Spragueville | Fairfield | existing |
| Springbrook | Jackson | existing |
| Springfield | | changed to Maquoketa in 1845 |
| Spruce Mills | Tetes des Mort |
| Sterling | Iowa | cemetery east of Miles |
| Sullivan | Prairie Springs |
| Summer Hill | Fairfield | changed to Spragueville |
| Tetes des Mort | Tetes des Mort | became St. Donatus |
| Union Center | | east of Maquoketa, had a church |
| Van Buren | Van Buren | also known as Buckeye |
| Wagonersburgh | Otter Creek | located at Otter Creek |
| Waterford | South Fork | Buckhorn area, has cemetery |
| Wickliffe | Washington | near Green Island |
| Zwingle | Otter Creek | existing, half in Dubuque County |
