identifiable, polymorphic region of DNA (i.e., marker) located to the side
of a gene (i.e., flanking), as opposed to an intragenic marker which is located
within the gene itself. Flanking markers are used in linkage analysis to
track the coinheritance of the gene in question.
Definition from: GeneReviews
from the University of Washington and the National Center for Biotechnology Information
See also Understanding Medical Terminology.