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While host gene expression has been related to symptoms associated with different phytoplasma diseases, it is unknown why some phytoplasmas are associated with different symptoms in genotypes of the same plant species. Pear tree selections showed symptoms of either leaf reddening (selection 8824-1) or leaf curling (selection 9328-1) associated with pear decline (PD) phytoplasma presence. PD populations were similar in leaves and shoots of the two selections, but in the roots, populations were significantly lower in selection 8824-1 than in 9328-1, indicating greater resistance. For host carbohydrate metabolism gene expression in PD-infected tissues, significant up-regulation in selection 8824-1 was observed for a sucrose synthase gene in leaves and an acid invertase gene in leaves and roots. These features have been associated with localized higher sugar levels in phytoplasma-infected tissues, and thus may be related to leaf reddening. For host stress/defense response gene expression in PD-infected tissues, significant up-regulation of a phenylalanine ammonia lyase gene was observed in PD-infected shoots of both selections; however, up-regulation of alcohol dehydrogenase gene in shoots, a chitinase gene in all tissues and a phloem protein 2 gene in roots was only observed for selection 8824-1. These changes indicate greater triggered innate immunity in roots associated with lower PD populations and leaf reddening. Leaf reddening may be related to changes in gene expression associated with increased sugar levels in leaves and stronger immune responses in several tissues, while leaf curling may be due to water stress resulting from dysfunctional root associated with higher PD populations in the roots.