Acid soils and low fertility are commonly associated with forested lands in Canada. This study reports results from analyses of growth, and genetic heterozygosity (using isoenzymes) among three lodgepole (Pinus contortavarlatifolia) populations at different elevations along the foothills of Alberta and their associations with microsite variation among 17 soil traits. Means of 14 of the 17 traits were different (P<=0.05) among locations; 9 of the 14 exhibited clinal trends with elevation. The first of two significant (P<=0.001) discriminant functions (DF1, DF2) accounted for 80% of the multivariate variance among the three sites. DF1, a general “site quality” function, was weighted most heavily by soil reaction (pH) while DF2 was best described by zinc and phosphorous. Tree growth was positively related to DF2 in the low‐ and mid‐elevation populations. The frequencies of significant (0.01<P<0.10) associations between genetic heterozygosity and soils‐microsites decreased with increasing elevation; only significant (P<=0.05) negative correlations were found between heterozygosity and tree growth, all at the lowest elevation.