Approximately 500 Tg of 2-methyl-1,3-butadiene (isoprene) is emitted by deciduous trees each year. Isoprene oxidation in the atmosphere is initiated primarily by addition of hydroxyl radicals (OH) to C-4 or C-1 in a ratio 0.57 +/- 0.03 (1 sigma) to produce two sets of distinct allylic radicals. Oxygen (O-2) adds to these allylic radicals either delta (Z or E depending on whether the allylic radical is cis or trans) or beta to the OH group forming six distinct peroxy radical isomers. Due to the enhanced stability of the allylic radical, however, these peroxy radicals lose O-2 in competition with bimolecular reactions. In addition, the Z-delta hydroxy peroxy radical isomers undergo unimolecular 1,6 H-shift isomerization. Here, we use isomer-resolved measurements of the reaction products of the peroxy radicals to diagnose this complex chemistry. We find that the ratio of delta to beta hydroxy peroxy radicals depends on their bimolecular lifetime (tau(bimolecular)). At tau(bimolecular) approximate to 0.1 Si a transition occurs from a kinetically to a largely thermodynamically controlled distribution at 297 K. Thus, in nature, where tau(bimolecular) > 10 s, the distribution of isoprene hydroxy peroxy radicals will be controlled primarily by the difference in the relative stability of the peroxy radical isomers. In this regime, beta hydroxy peroxy radical isomers comprise similar to 95% of the radical pool, a much higher fraction than in the nascent (kinetic) distribution. Intramolecular 1,6 H-shift isomerization of the Z-delta hydroxy peroxy radical isomers produced from OH addition to C-4 is estimated to be similar to 4 s(-1) at 297 K. While the Z-delta isomer is initially produced in low yield, it is continually reformed via decomposition of the beta hydroxy peroxy radicals. As a result, unimolecular chemistry from this isomer contributes about half of the atmospheric fate of the entire pool of peroxy radicals formed via addition of OH at C-4 for typical atmospheric conditions (tau(bimolecular) = 100 s and T = 25 C). In contrast, unimolecular chemistry following OH addition at C-1 is slower and less important.