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Phenylalanine ammonia lyase (PAL) is a key enzyme of the phenylpropanoid pathway. PAL genes are less extensively studied in gymnosperms than angiosperms. Our interest in the PAL genes in Pinus taeda stems from their potential role in pine defense mechanisms. Despite the number of characterized gymnosperm PAL genes, the functional diversity of these and the extensive transcriptome data available for Pinus taeda, only one PAL gene had been characterized in P. taeda. Here, we present an extensive phylogenomics analysis of the PAL gene family in P. taeda including identification of five distinct paralogs. Assembly coverage and expression profiles are variable among the five PAL genes in P. taeda. A phylogenetic analysis revealed a unique evolutionary history for the PAL genes in gymnosperms including origin of a distinct "gymnosperm" PAL gene clade. A reconciliation method was used to map ancestral duplication events and lineage-specific duplication. Molecular evolutionary analysis of the gymnosperm genes showed shifts in selective constraints following gene duplications.