Hudson is an Evolutionary Biologist primarily interested in microorganisms. He has studied the adaptive advantage of natural genetic transformation in bacteria—a process that involves the replacement of a cell’s own genes by those from another individual. He has also investigated why slime mold ameobas make a greater sacrifice—giving up their lives—to enhance the dispersal of other individual cells that may not be their relatives. Hudson's main current interest concerns the clay hypothesis for the origin of life, which postulates that populations of tiny inorganic crystals can evolve by natural selection, given that they have variation in growth rates that may be due to heritable surface defects.

Hudson, R. E., U. Bergthorsson, and H. Ochman, 2003. Transcription Increases Multiple Spontaneous Point Mutations in Salmonella enterica. Nucleic Acids Research 31 (15): 4517-4522. Hudson, R. E., J. E. Aukema, C. Rispe, and D. Roze, 2002. Altruism, Cheating, and Anti-Cheater Adaptations in Cellular Slime Molds. American Naturalist 160 (1): 31-43.