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Increases in pathogenesis-related (PR) transcripts are commonly interpreted as evidence of plants’ resistance responses to pathogens; however, few studies have examined whether increases in PR proteins protect plants growing under natural conditions. Pseudomonas syringae pv. tomato DC3000, which is virulent and causes disease in Arabidopsis, is also pathogenic to the native tobacco Nicotiana attenuata. N. attenuata responds to R syringae pv. tomato DC3000’s challenges with increases in salicylic acid and transcripts of at least two PR genes, PR-1 and PR13/Thionin. To determine if either of these PR proteins functions in bacterial resistance, we independently silenced both genes by RNAi and found that only PR-13/Thionin mediates resistance to R syringae pv. tomato DC3000 in glasshouse experiments. When NaPR-1- and NaThionin-silenced plants were transplanted into the plant’s native habitat in the Great Basin Desert of Utah, opportunistic Pseudomonas spp. performed better on NaThionin-silenced plants compared with NaPR-1-silenced and wild-type (WT) plants, and accounted for increased plant mortality. The native herbivore community of N. attenuata attacked both NaPR-1- and PR-13/NaThionin-silenced plants to the same degree as it did in WT plants, indicating that neither PR protein provides resistance to herbivores. Although PR-1 is generally considered a marker gene of disease resistance, we found no evidence that it has an antimicrobial function. In contrast, PR-13/NaThionin is clearly an ecologically relevant defense protein involved in resisting pathogens in N. attenuata.