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22.	Report to Hayden. United States Geological and Geographical Survey of the Territories. 1870.
23-26. Report to Hayden. 1871-1873.
27.	Monograph of the Cretaceous Flora of the Dakota Group. 1874.
28.	Review of the Fossil Flora of North America. (Republished, with corrections, in the Penn Monthly.) 1875.
29.	Article on Coal and Coal Flora. Encyclopædia of North America.
30.	Text (Latin) of Sullivant's Supplement to the Icones. 1874.
31.	On Some New Species of Fossil Plants, Tertiary. Bulletin 52, second series of Hayden. 1875.
	On Some New Species of Fossil Plants, Cretaceous. 1875.
32.	Report on the Cretaceous and Tertiary Floras of the Western Territories. Hayden's Report, and separate copies. 1874.
33.	Species of Fossil Marine Plants found in the Carboniferous Measures. Geological Survey of Indiana, Seventh Annual Report. 1876.
34.	Plants of the Silurian. Proceedings of the Philosophical Society of Philadelphia. 1877.
35.	Contributions to the Fossil Flora of the Western Territories. United States Geological and Geographical Survey. The Tertiary Flora. 1877.
36.	Pliocene Flora of the Auriferous Gravel of California. Museum of Comparative Zoölogy, Cambridge. 1878.
37.	Catalogue of the Fossil Plants of the Tertiary and of the Cretaceous. Hayden's Report. 1878.
38.	On Cordaites. American Philosophical Society. 1878.
39.	On a Branch of Cordaites bearing Fruit. American Philosophical Society. 1879.
40.	The Coal Flora (Atlas). Second Pennsylvania Geological Survey. 1879-1884.
41.	The Coal Flora (text). Three volumes. 1880-1884.
42.	Manual of the American Mosses. With Collaboration of Thomas P. James. 1884.
43.	Monography of the Cretaceous and Tertiary Flora of the United States. Geological and Geographical Survey of the Territories, vol. viii. 1883.
44.	Principles of Palæozoic Botany. Geological Report of Indiana. 1884.
45.	Vegetable Origin of Coal. Report of Geological Survey of Pennsylvania. 1885.
46.	Divers Questions concerning Coal. Silliman's Journal. 1860.
	On the Fossil Fruits of the Lignites of Brandon. 1861.
	On Some Fossil Plants of the Recent Formations. 1859.
	On Some Fossil Plants of John Evans. 1859.
	On the Origin and Formation of the Prairies. 1865.
	On the Formation of Lignite Beds. 1874.
	On Land Plants in the Lower Silurian. 1874.