We studied isozyme variation at 21 loci in 66 populations from three s
ubspecies of Pinus contorta Dougl.; 35 in spp. latifolia, 20 in spp co
ntorta and 11 in spp. murrayana. The objectives were to assess gametic
disequilibria and multilocus structure. There was considerable differ
entiation of allele frequencies at 19 polymorphic loci across the 66 p
opulations and within the subspecies. Allele frequencies at many loci
correlated with geographic variables. Genetic variability varied consi
derably among populations within subspecies but the subspecies means w
ere similar. The mean number of polymorphic loci and the mean heterozy
gosity over 19 polymorphic loci were, respectively, 13 and 0. 194 in l
atifolia, 12 and 0. 196 in murrayana, and 12 and 0.180 in contorta. Th
e mean heterozygosity correlated with longitude and altitude across th
e 66 populations and with latitude in latifolia. Gametic disequilibria
were evident in 40 populations; 29 in latifolia, eight in murrayana a
nd three in contorta. Gametic disequilibria correlated with latitude a
cross the 66 populations and with longitude in latifolia. The single-l
ocus F(ST) averaged 0.0339 in latifolia, 0.0567 in murrayana, and 0.07
64 in contorta. The multilocus F(STM) was 0.1227 in latifolia, 0.2926
in murrayana, and 0.3328 in contorta. Multilocus Wahlund and founder e
ffects, migration patterns, and natural selection, probably played sig
nificant roles in generating and maintaining the multilocus genetic st
ructure in P. contorta in general and the subspecies latifolia in part
icular.