The relationship of this species with the very similar species P. armandii, P. fenzeliana and P. morrisonicola and the infraspecific taxa in this group of East Asian pines belonging to subsection Strobus is in need of further investigation using DNA sequence data. Pinus amamiana may be most distinct in its cones and seeds, which seem to be more morphologically adapted to seed dispersal by birds and rodents, with small cones and relatively large, virtually wingless seeds. However, from DNA analysis of other pines with such cones (e.g. P. albicaulis and P. cembra) strong selective pressure has determined the evolution of these adaptations and they are not necessarily good indicators of phylogenetic relationships.
No recent uses have been recorded of this species; in the past its timber was exploited and used locally for construction, carpentry and wooden canoes for fishermen. It is reported to be very rare in cultivation, but since it has frequently been referred to as P. armandii var. amamiana or even equated with that species (as it was considered by E. H. Wilson, 1916), there may be trees in collections (arboreta etc.) that are misidentified. It may be somewhat more common in Japanese gardens.