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Merrill, F.J.H., 1890. On the Metamorphic Strata of Southeastern New. York. American Journal of Science 39, 383-392.
Merrill, F.J.H., 1891. A Guide to the Study of the Geological Collections of the NYS Museum, New York State Museum Bulletin. The University of the State of New York, Albany, New York.
Merrill, F.J.H., 1893. Salt and Gypsum Industries of New York, New York State Museum Bulletin. The University of the State of New York, Albany, New York.
Merrill, F.J.H., 1895. Mineral Resources of New York State, New York State Museum Bulletin. The University of the State of New York, Albany, New York.
Merrill, F.J.H., 1897. Road Materials and Road Building in New York, New York State Museum Bulletin. The University of the State of New York, Albany, New York.
Merrill, F.J.H., 1899. Origin of the White And Variegated Clays of the North Shore of Long Island. Annals of the New York Academy of Sciences 12, 113-116.
Merrill, F.J.H., 1902. Description of the State Geologic Map of 1901, New York State Museum Bulletin. The New York State Education Department, Albany, New York.
Merrill, F.J.H., Clarke, J.M., 1902. Report of the State Paleontologist 1901, New York State Museum Bulletin. The University of the State of New York, Albany, New York.
Merrill, F.J.H., 1903. Natural History Museums of the United States and Canada, New York State Museum Bulletin. The University of the State of New York, Albany, New York.
Merrill, F.J.H., Clarke, J.M., 1903. Report of the State Paleontologist 1902, New York State Museum Bulletin. The University of the State of New York, Albany, New York.
Merrill, F.J.H., 1905. Cyanide of Potassium. Science 22, 568.
Merrill, F.J.H., 1905. Maps of Mexico. Bulletin of the American Geographical Society 38, 281-287.
Merrill, F.J.H., Clarke, J.M., 1903. Report of the State Paleontologist 1902, New York State Museum Bulletin. The University of the State of New York, Albany, New York.
Merrill, F.J.H., Clarke, J.M., 1901. Paleontologic Papers 2, New York State Museum Bulletin. The University of the State of New York, Albany, New York.