Funding for fieldwork dried up and he instantly became a foreigner in the new state of Tajikistan at a time when ethnic Russians were fleeing Central Asia en masse.
Marshak stayed on as director of the excavation of the Panjakent ruins, even during the years of civil war in Tajikistan from 1992 to 1997, while other archeological sites in the former Soviet Union were plundered by looters.
Through close cooperation with the government of Tajikistan, Marshak ensured protection and continued excavation of the Panjakent site.
In the 1990s and first decade of the 21st century Marshak received numerous honorariums from international organizations and taught, lectured and conducted fellowships in Italy, the United States, Austria and elsewhere.
[2] His wife, the noted archeologist and Marshak's frequent professional collaborator, Valentina I. Raspopova, later resumed her excavation work at the site.