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Currently, the studies of the influence of anthropogenesis on the changes in physical and physico-chemical properties of soils experience a notable shift. Apart from traditional approaches to determining the properties of the bulk soil, the new information level is to determine soil aggregate structures including the evaluation of changes at the meso- and microaggregate levels. Determination of thermal diffusivity of soils and the assessment of the degree of influence of such factors as moisture content, particle size, and mineralogical composition, as well as organic matter content, is one of the most relevant tasks of agrophysics and physics of soils. Commonly, such an experimental analysis is carried out for either the native material or under the conditions of lysimetric experiments. There are also several mathematical models for calculating thermal properties of soils depending on the factors listed above. Application of the methods of thermooptical spectroscopy is a promising instrument for more delicate measurement and modeling of the dependence of thermal properties of soil on its physical and elemental composition, moisture, porosity, and density. Also, thermooptical spectroscopy can be on demand for studies of changes of properties of entities of different hierarchical level under the action of agrogenesis and anthropogenesis. In this study, we used photothermal-deflection spectroscopy (PDS) for estimating thermal diffusivity of various types of soil and soil aggregates. The setup was built with a high-power He–Ne laser (632.8 nm, 35 mW) as an excitation beam and a green He–Ne laser (543.1 nm, 2 mW) as a probe. We have shown that PDS clearly distinguishes between thermal diffusivities of different soil types (soddy-podzolic, 29.5 ± 0.2; chernozem, 11.1 ± 0.2; and gray soils, 8.6 ± 0.5 cm2/h) even for low amounts of the test material and the size of the aggregates (a 3 × 3 mm surface). The results are in good agreement with the calculations and the existing data [1]. Microaggregates of chernozem soil show a significantly higher thermal diffusivity compared to the bulk soil; and for untreated and arable soil samples, thermal diffusivities of microaggregates differ significantly: 51.5 ± 0.5 and 46.2 ± 0.5 cm2/h, respectively. Aggregates of different soil horizons within the same soil profile (topsoil, depth 10–13 cm, and an illuvial horizon, depth 180–185 cm) also show a significant difference, thermal diffusivities are 12.3 ± 0.4 and 24 ± 2 cm2/h, respectively. For soil aggregates, PDS is capable to distinguish the difference in thermal diffusivity accounted for by the changes in the structure of aggregates.