The Chernobyl Exclusion Zone (CEZ) represents a unique natural laboratory that received significant 129I contamination across a range of soils and land-use types in a short time period in 1986. Data are presented on 129I and 127I in soil samples collected from highly contaminated areas in the CEZ in 2015. The geometric mean (GM) total concentration of stable iodine (127I) was 6.7 × 10−7 g g−1 and the (GM) total concentration of 129I was 2.39 × 10−13 g g−1, equivalent to 1.56 mBq kg−1. GM total 127I concentration is below the European average soil concentration of 3.94 × 10−6 g g−1, while 129I is significantly higher than the pre-Chernobyl activity concentration for 129I of 0.094 mBq kg−1. Significant differences were found in the extractability of native, stable 127I and 129I almost 30 years after the introduction of 129I to the soils. Both 127I and 129I were predominantly associated with alkaline-extractable soil organic matter, established using a three-step sequential extraction procedure. Whereas 127I was significantly correlated with gross soil organic matter (measured by loss on ignition), however, 129I was not. The ratio of 129I/127I was significantly lower in extracts of soil organic matter than in more labile (soluble and adsorbed) fractions, indicating incomplete equilibration of 129I with native 127I in soil humic substances after 29 years residence time in the CEZ soils. The initial physico-chemical form of 129I in the CEZ soils is unknown, but the widespread presence of uranium oxide fuel particles is unlikely to have influenced the environmental behaviour of 129I. Our findings have implications for long-term radiation dose from 129I in contaminated soils and the use of native, stable 127I as a proxy for the long-term fate of 129I.