Report on the insects collected on the Penobscot and Alleguash Rivers, during August and September, 1861, Sixth Annual Report of the Secretary of the Maine Board of Agriculture, Augusta, Maine (pp. 373-376) (1861)
Guide to the Study of Insects (1869; third edition, 1872)
The Mammoth Cave and its Inhabitants (1872), with F. W. Putnam
Life-History of Animals (1876)
A Naturalist on the Labrador Coast (1891)
Lamarck, the Founder of Evolution: His Life and Work (1901), French translation, 1903.