New data sets and analytic techniques provide the tools to build a new perception of changes in the New England flora following the retreat of the last Pleistocene continental glacier. We consider a set of 13 species for which genetic data are available in the context of 1) the fossil record when available, and 2) the evidence of the distribution of appropriate habitat in the late Pleistocene and Holocene. The current New England flora is derived from a diverse set of refugia including the High Arctic, the serpentines of the American West, and the unglaciated and now submerged North Atlantic coastal plain as well as the traditional refugia to the south, both along the coastal plain and to the west in the lower Mississippi valley. This analysis demonstrates that present-day communities are in fact transient, constantly changing assemblages of species.