This plant was described in 1910 by Michel Gandoger in the bulletin of the French Botanical Society at species rank. It took over half a century when it was reclassified as a subspecies of Juniperus oxycedrus (Amaral Franco, 1963) and later treated at variety rank under the same species (John Silba, 1984).

In the monograph of Cupressaceae and Sciadopitys (2005) Aljos Farjon also treated it at subspecies rank. Soon, Robert P. Adams, referring to sequence data, restored its species status and allied it with Juniperus brevifolia of the Azores – an idea that we have had earlier (based on the plant's morphology and general appearance) but did not publicize. An unique juniper that needed a thorough documentation so we visited its stands in southern Portugal in 1995 and then in 2008.

In a lowland habitat near Azeitão it occurs in (somewhat secondary) pine forest of Pinus pinaster accompanied by Erica lusitanica, Lavandula stoechas, Phillyrea latifolia, Quercus suber, Ulex europaeus and other common atlanto-mediterranean plants. Some small shrubs of Juniperus navicularis, turning the adaxial sides of their needles upward, can be quite silvery, others (mainly those with pendent branchlets) are less so. The cones are globose or subglobose (in 2008 we found a specimen that had unusual, somewhat pear-shaped, cones as shown by a photo below). The tallest specimen of this juniper we encountered was about 3 m high with a stem diameter of 8 cm.