 In 1989 McFall-Ngai accepted a position and later received tenure at the University of Southern California in the Department of Biology and began breeding and studying the Hawaiian bobtail squid.She and Ruby moved to Hawaii in 1996 to better study the squid-bacteria relationship, both accepting positions at Pacific Biomedical Research Center at the University of Hawaii.In 2004, McFall-Ngai accepted a position as professor in the Department of Medical Microbiology and Immunology at the University of Wisconsin–Madison and the Eye Research institute.