The Museum is the repository for some major regional collections. It also maintains a large collection of floral and faunal specimens from Baja California as the result of the College's long and continued maintenance of research sites in the Mexican state.

Entomology

• Coleoptera
• Culicidae Collection: Dr. Donald R. Brothers
• Idaho National Laboratory Formicidae Collection
• Lepidoptera Collection: Carl Cannon
• Lepidoptera Collection: Robert Chehey
• Mecoptera
• South Central Idaho General Entomology Collection: Dr. Paul Castrovillo
• Strepsiptera
• Trogidae Collection: Dr. Charles W. Baker

Archaeology

• Luther Douglas Navajo Ceremonial Sandpaintings Collection
• The Gates-Lewis Collection  -  An Enduring Presence
• The Olga Gonzalez Pre-Columbian Collection
• Hopi Basketry and Pottery Collection
• The James Huntley Native American Lithic Collection
• The Meldrum New Guinean/New ZealandCollection
• The Troxell Collection
• The Warm Springs Site, Boise, Idaho

Fossil

• Succor Creek, Idaho Collection
• Green River Formation Collection
• Bake Young Collection
• Ichthyology Collections
• The College of Idaho Collection
• Idaho Department of Environmental Quality Collection: Beneficial Use Reconaisance Program
• Idaho Department of Fish and Game Collection
• Richard L. Wallace Collection (formerly at University of Idaho)
• US Bureau of Land Management Collection
• US Bureau of Reclamation Collection
• US Environmental Protection Agency EMAP/REMAP Collection
• US Forest Service Collection
• US Geologic Survey Idaho Water Science Collection

Aquatic Invertebrates

• Idaho Dept of Environmental Quality: Beneficial Use Reconaisance Program; statewide 1994-2007
• Idaho Power Company: Middle Snake River Aquatic Inverebrate Samplings
• US Bureau of Reclamation: 1995-2007 Upper Snake River Snail Samplings

Mollusca

• Freshwater Gastropoda: Middle and Upper Snake River
• Freshwater Bivalvia: Iowa 1983-1987; Dr. Terrence J. Frest Collection
• Welty Fossil Collection
• Marine Mollusca: Baja California, Mexico: Bratz Family Collection
• Marine Mollusca: Australia: Al Walrodt Collection
• Marine Mollusca: Worldwide: Bender Collection

Baja California Research

• Botany
• Entomology
• Reptiles

Library

• General Reference Library
• Ira LaRivers Library
• Thomas Lugasky Library

Other Associated C of I Collections

• Evans Gem and Mineral Collection
• Tucker Herbarium
• Whittenberger Planetarium