The majority of the previous studies on the faunal structure and dynamic were carried out on calcareous scree slopes, and a few descriptive studies were conducted on fauna inhabiting the MSS on other geological substrates. Here, we analyzed the invertebrate communities from the MSS developed in calcareous substrate and in crystalline schists. We investigated how the environmental conditions in two different geological substrates influence the spatial distribution of invertebrate communities over time. We sampled invertebrate species, monthly, in both geological substrates, at different altitudes, depths and types of scree slopes (covered and nude screes). We identified a total of 99 invertebrate species. Canonical correspondence analysis indicated a strong correlation of the calcareous geological substratum with an invertebrate species assemblage. Calcareous substratum, altitude, exterior temperature, relative humidity and the type of gravel were identified as the main factors influencing community structure. The crystalline schists are inhabited by a heterogeneous community of species (cryphilous species or opportunistic species) and are mainly influenced by altitude and exterior relative humidity. The complex environmental conditions of Leaota Mountains emphasized that the calcareous geological substratum is an important abiotic factor that influence the structure of the invertebrate community of MSS.