In 1995 she was awarded a Fulbright Program fellowship, which allowed her to pass a semester at the Monterrey Institute of Technology, Campus Guaymas, in Sonora, where she conducted long-term studies on natural populations of cactophilic Drosophila.
In 1999, Markow moved to the University of Arizona in Tucson as Regents’ Professor of Ecology and Evolutionary Biology and Director of the Center for Insect Science.
Markow joined University of California, San Diego in 2008, where she was appointed Amylin Chair in Life Sciences and continued as Director of the Drosophila Species Stock Center which moved with her to UCSD.
Her research recently has focussed upon use of ecological diverse Drosophila species as a models to understand public health problems such as diabetes and obesity.
In response to the misuse of their genetic data, the Havasupai people issued a "banishment order" to keep Arizona State University employees from setting foot on their reservation.
In 2010, The Arizona Board of Regents settled the case in an attempt to “remedy the wrong that was done.” They agreed to pay the Havasupai $700,000, as well as return the collected blood samples.