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In Matsalu National Park a flood is a natural disturbance which shapes ecosystems and communities. The impact of human activities (e.g. extensive mowing once a year or low stress grazing) on the habitat in this area is low. The disturbances are caused by natural conditions such as melting snow, precipitation and brackish sea water and the presence of flood is supported by flat relief. The aim of the current study was to describe the Chilopoda and Diplopoda assemblages of semi natural meadows and to find out the effect of habitat conditions on these invertebrates. On the 12 studied meadows we sampled and analysed soil invertebrates by using pitfall traps in the non-flooded and flooded areas of meadows. The individuals of 10 Chilopoda species and 15 Diplopoda species, which assemblages were more abundant and diverse in the non-flooded areas of meadows with trees and bushes nearby, were collected on semi natural meadows in Matsalu. Only a few species were represented in abundance on studied meadows including Leptoiulus proximus, L. cibdellus, Julus terrestris, J. scanicus. The species Pachymerium ferrugineum, Schendyla nemorensis, Julus terrestris, J. scanicus, Leptoiulus cibdellus, Xestoiulus laeticollis were also found in the areas flooded with brackish water. The activity density and species richness of Chilopoda and Diplopoda were significantly lower in the flooded areas of the meadow after flood water withdrawal compared to the non-flooded areas of the same meadows.