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The best map collections for Idaho are at libraries of Boise State University and Idaho State University. The Family History Library in Salt Lake City has a small collection of maps for the territories of Oregon and Idaho.
The following publications include maps that can aid your research:
Preston, Ralph N. Maps of Early Idaho.(Corvallis, Oregon: Western Guide Publishers, 1972. FHL book Q 979.6 E3p.) Lists early towns, gold mines, and old military roads.
An Atlas of Idaho Territory, 1863-1890. ([Boise, Idaho]: Idaho Historical Society, 1978. FHL book Folio 979.6 E7a.)
Printable maps are also available from the National Atlas of the United States -- http://nationalatlas.gov/printable.html