Numerous studies show that pharmacological inhibition of p38 mitogen-activated protein kinases (p38s) before lethal ischemia prevents conditioning. However, these inhibitors have off-target effects and do not discriminate between the alpha and beta isoforms; the activation of which is thought to have diverse and perhaps opposing actions with p38α aggravating, and p38β reducing, myocardial injury. We adopted a chemical genetic approach using mice in which either the p38α (DRα) or p38β (DRβ) alleles were targeted to substitute the “gatekeeper” threonine residue for methionine, thereby preventing the binding of a pharmacological inhibitor, SB203580. Isolated, perfused wild-type (WT), DRα and DRβ mouse hearts underwent ischemic preconditioning with 4 cycles of 4 min ischemia/6 min reperfusion, with or without SB203580 (10 µM), followed by 30 min of global ischemia and 120 min of reperfusion. In WT and DRβ hearts, SB203580 completely abolished the reduction in myocardial infarction seen with preconditioning and also the phosphorylation of downstream substrates of p38. These effects of SB203580 were not seen in DRα hearts. Furthermore ischemic preconditioning occurred unaltered in p38β null hearts. Contrary to expectation the activation of p38α, and not p38β, is necessary for ischemic preconditioning. Since p38α is also the isoform that leads to lethal myocardial injury, it is unlikely that targeted therapeutic strategies to achieve isoform-selective inhibition will only prevent the harmful consequences of activation.