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We asked whether (a) variation in species composition of parasite assemblages on the same host species follows a non-random pattern and (b) if so, manifestation of this non-randomness across space and time differs among parasites, hosts and scales. We assessed nestedness and its contribution to β-diversity of fleas and gamasid mite assemblages exploiting small mammals across three scales: (a) within the same region across different locations; (b) within the same location across different times and (c) across distinct geographic regions. We estimated (a) the degree of nestedness (NCOL) and (b) the proportional contribution of nestedness to the total amount of β-diversity across locations, times and regions (βNESP). In the majority of host species, parasite assemblages were nested significantly across all three scales. In mites, but not fleas, NCOL correlated with the contribution of nestedness to the total amount of β-diversity. In fleas, NCOL did not differ among assemblages at the two local scales, but was significantly lower at regional scale. In mites, NCOL was the highest in assemblages at local spatial scale. βNESP was significantly higher (a) in flea than in mite assemblages at both local scales and (b) in mite than in flea assemblages at regional scale. In fleas, βNESP was higher at both local scales, whereas in mites it was higher at both local temporal and regional scales. Sheltering habits and geographic range of a host species did not affect either NCOL or βNESP in flea assemblages, but both metrics significantly decreased with an increase of geographic range of a host species in mite assemblages. We conclude that flea and mite assemblages across host populations at smaller and larger spatial scales and at temporal scale were characterized by nestedness which, in turn, contributed to an important degree to the total amount of β-diversity of these assemblages.