Sampson was fired last week for "inappropriate and unacceptable" behaviour in a previous role at the Bristol Academy. A decision on a permanent successor is due in the New Year.
Marley, 50, has been in charge of the under-19 side and will now guide the team for a friendly against France next month and two November home women's World Cup qualifiers against Bosnia & Herzegovina and Kazakhstan.
"Mo was the obvious choice to take over the team as she has in-depth knowledge of the women’s game and importantly knows the players well," said FA technical director Dan Ashworth in a statement.
England were third in the 2015 World Cup in Canada and reached the semi-finals of this year's European Championship in the Netherlands.
(Reporting by Alan Baldwin, editing by Ken Ferris)
