In recent decades, various isotopic methods have been widely used to study trophic relationships in soil ecosystems, because the isotopic signature of heterotrophic organisms reflects the isotopic composition of their preferred food objects. The composition of carbon (delta C-13) and nitrogen (delta N-15) isotopes of biological objects is most often used in such environmental research. However, the correct use of the method to reconstruct detrital food webs is often hampered by the individual (within the body) variability of the carbon and nitrogen isotopic composition in the tissues and organs of many groups of soil invertebrates. The goal of this study is to compare the individual variability of isotopic composition of various tissues and organs of common Mediterranean species of woodlice (Armadillo officinalis, Armadillidae, Isopoda and Armadillidium vulgare, Armadillidiidae, Isopoda) and the Mediterranean banded centipede (Chilopoda, Scolopendromorpha, Scolopendra cingulata). Soil invertebrates were collected on the territory of the Utrish State Natural Reserve (Krasnodar krai, Russia). Isotopic analyses were performed for the exoskeleton, muscles, intestinal walls, fat body (only for centipedes), reproductive system, legs, and a whole, homogenized body. The isotope composition of delta C-13 and delta N-15 was estimated with a set of equipment consisting of an elemental analyzer and an isotope mass spectrometer. The differences in delta C-13 between the tissues of woodlice reached 5-6 parts per thousand due to the incorporation of inorganic carbonates in the exoskeleton. The tissues of the banded centipede showed no significant difference in their isotopic composition. The trophic position of the large woodlouse species can be best characterized by the isotope analysis of muscle tissues. The use of limbs is possible only after preliminary assessment of the carbonate content in the integumentary tissues of the species. The homogenization of large species is unfavorable, as well as the remains of exoskeleton fragments and food debris in the analyzed sample. For centipedes, one can use not only muscles but also homogenized samples of the whole body, as well as individual parts of the body and organs, excluding the gut contents. The results are applicable for the optimization of soil-zoological studies via isotopic analysis of the tissues of various invertebrates.