In lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia Engelm.), cone bud initiation within long-shoot buds varies according to genotype. We chose to study hormone profiles of two genotypes that differed significantly in cone yield. Phytohormone profiles were established by high performance liquid chromatographyelectrospray ionization tandem mass spectrometry in multiple reaction monitoring mode with samples collected from genotypes 299 and 233, the typically high and low cone producers. Generally, concentrations of trans-zeatin-Oglucoside were higher in genotype 299, whereas dihydrozeatin concentrations were higher in genotype 233. Both isopentenyl adenine and isopentenyl adenosine were present at higher concentrations in genotype 233. The ratio of total quantifiable zeatin (Z)-type cytokinins to isopentenyl (iP)-type cytokinins was approximately threefold higher in genotype 299 during female cone bud differentiation. In genotype 299, ABA concentration was significantly lower than in genotype 233 on the first sampling date, while the phaseic acid concentration was lower consistently throughout the period investigated. Dihydrophaseic acid was present in low concentrations in most samples of genotype 233, but was not quantifiable in genotype 299. Our study reveals that long-shoot buds of the high cone-producing genotype had higher ratios of Z-type cytokinins to iP-type cytokinins than were found in the low cone-producing genotype. High coneproducing buds also contained less ABA, phaseic acid and dihydrophaseic acid during female cone bud differentiation.