Under Brooks, Morgan completed his thesis work on the embryology of sea spiders—collected during the summers of 1889 and 1890 at the Marine Biological Laboratory in Woods Hole, Massachusetts—to determine their phylogenetic relationship with other arthropods. He concluded that with respect to embryology, they were more closely related to spiders than crustaceans. Based on the publication of this work, Morgan was awarded his Ph.D. from Johns Hopkins in 1890, and was also awarded the Bruce Fellowship in Research. He used the fellowship to travel to Jamaica, the Bahamas and to Europe to conduct further research.