Paleolimnology is a rapidly expanding field within the natural sciences. To date, many scientific papers have been published focusing on studies of remains from single sediment cores in specific lakes, or a few cores from the same water body. However, few previous publications have provided a comprehensive comparative analysis of taphocenosis (and maternal community) changes in different water bodies from a large geographical region during whole Holocene using multivariate statistical methods. We conducted a joined statistical analysis of data obtained as a result of the cladoceran analysis of the sediment samples from six cores taken along the North-South transect from the Kola Peninsula to the Karelian Region (North-West Russia). Our aim was to identify, based on quantitative statistical methods, general whole-Holocene patterns in cladoceran taphocenosis changes. All taphocenoses in all cores from six lakes can be classified into six clusters based on their species composition. Our unexpected conclusion is that different taphocoenoses are formed by the same set of species, but their proportions vary significantly. This suggests that the same species may play different functional roles in different maternal communities. During whole Holocene, we observed a single taphocenosis cluster in the Holocene core from Lake Antyukh-Lambina, and four taphocenosis clusters in the Lake Medvedevskoe, with an intermediate number of clusters in the lakes between them. Furthermore, it can be asserted that the potential for cluster changes in the core is greater for the more southern studied water bodies (0–3 clusters for northern lakes vs. 4 clusters for southern lakes). Based on our data, we hypothesize that the diversity of cladoceran associations during the Holocene was lower in Arctic/Subarctic lakes, possibly due to their formation by ubiquitous species. Our study suggests that at least some Arctic lake ecosystems have remained unchanged since deglaciation times. Further studies are necessary to determine if this is a general rule.