Needle dimensions and stomate densities were measured for 300 seedlings representing a stratified sampling of 30 families of whitebark pine (Pinus albicaulis) from California, Oregon, Washington, Idaho, and Montana (USA), and British Columbia (Canada). The seedlings were selected from a larger common garden trial examining white pine blister rust (WPBR) resistance of 225 families from populations representing much of the geographic range of whitebark pine. The objective was to examine variation in needle characteristics, including needle width, number of stomata, and stomate density, and their relation to WPBR infection. Two cohorts of needles were sampled-2008 and 2009-and morphological characteristics on both adaxial (AD) and abaxial (AB) surfaces were measured. Averaged over families and blocks, all traits except needle width were larger for the 2009 cohort, and within a cohort, averages were greater for variables measured on the AD surface relative to the AB surface. Mean stomate densities (ADEN, stomata mm-2) ranged from 29.30 to 40.57 on the AD leaf surface and from 13.75 to 22.52 on the AB leaf surface for the 2008 cohort. These values were moderately correlated with stomate densities on the same needle surfaces in the 2009 cohort (r = 0.543, p = 0.002 and r = 0.565, p = 0.001 for AD and AB sides, respectively). ADEN for the 2009 needle cohort ranged from 38.77 to 52.22 on the AD surface, and from 18.82 to 29.86 on the AB surface. Family means for needle width (NW) ranged from 0.773 to 1.022 mm for the AD surface, and from 0.886 to 1.197 mm for the AB surface across cohorts. Mean numbers of rows of stomata, stomate abundance, and stomate density by needle length were significantly correlated with NW on the AD surface. Stomate density within rows (RDEN) showed a moderate and significant correlation for the 2009 cohort with number of needle spots resulting from the artificial inoculation with blister rust spores (r = 0.543, p = 0.002 and r = 0.438, p = 0.015 for AD and AB, respectively); RDEN was significantly correlated with mean temperature in the warmest month. In addition, the number of stomate rows was negatively correlated with early canker development (number of cankers) as well as growing season and spring precipitation at the seed source. These results suggest that source climate may influence rust symptom development via stomate traits that are under adaptive selection.