Cedrus is a long-lived forest tree whose extant distribution is limited to a disjunct occurrence at the southern margin of the wide expansion range of its family Pinaceae. Its taxonomy is marked with conflicting inferences. The position of Cedrus within Pinaceae is unresolved between the major subfamily groupings. The infrageneric classification of Cedrus taxa, which is based on indistinct phenotypic characters, remains highly controversial. Within its narrow geographical boundaries, Cedrus has long been, and is still, threatened with a diversity of degrading pressures that raise questions on the viability of the dispersed remnant populations. The unsettled taxonomic dispute, compounded with gaps and uncertainties in the information available on the genus, impede potential efforts toward the conservation and sustainable management of this ancient heritage. This study employed molecular systematics to establish a better understanding of the phylogenetic relationships of Cedrus at the different organizational levels from genus to species and populations. The phylogeny of Pinaceae, reconstructed from chloroplast DNA sequences, establishes Cedrus as a monophylum and resolves its position as sister to the rest of the Pinaceae genera. A DNA-based phylogeny of the interrelationships within Cedrus delimits five evolutionary units which are recognized as species, emphasizing the significance of their geographical disjunction. The evolutionary sequence of these units defines an east-west migration trend from the Himalayas toward the Mediterranean. At the population level, fingerprinting of the genetic diversity in the remnant Cedrus isolates of Lebanon infers a substantial level of diversity distributed within populations with no indication of interpopulation divergence. These findings are instrumental at defining the future conservation of Cedrus as a genetic resource