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We calculate the spatial variation in species richness, taxonomic beta diversity, and alpha and beta phylogenetic diversity (PDαandPDβ, respectively) of Atlantic Forest harvestman communities using a data set containing 556 species from 68 sites, distributed in 12 Brazilian states.

We compare the congruence of phylogenetic and taxonomic diversity patterns, and also comparePDαwith null model expectations, to check for phylogenetic clustering or overdispersion in communities.

Species richness andPDαare correlated, peaking in southern and south‐eastern coastal sites and decreasing towards the interior and towards the north‐east.PDαin north‐eastern sites was higher than expected, while a clustered phylogenetic pattern characterised most other sites.

Communities in the southern and south‐eastern regions were dominated by species from the large family Gonyleptidae, presenting a high richness and a lowPDα. As the dominance of Gonyleptidae decreased towards the north, where local communities have fewer species, but a higherPDα, they contain representatives of other families. The beta diversity was more sensitive to the compositional changes involving closely related Gonyleptidae species, whilePDβis more influenced by deeper phylogenetic compositional changes, between more distant lineages.

Phylogenetic diversity may be of special importance to assess the conservation value of distantly related lineages. These species‐poor groups are less likely to influence taxonomic‐based diversity analyses, but their importance for conservation arises from their phylogenetic distinctiveness, captured byPDαandPDβmeasures.