Heat shock proteins (Hsps) can help organisms to survive environmental stresses. Tardigrades are aquatic metazoans able to colonize unpredictable, or “hostile to life”, terrestrial habitats entering resting stages such as cysts and anhydrobiotic tuns. In this paper we compared the Hsp70 and Hsp90 expression between resting stages (tuns or cysts) and active hydrated specimens of two eutardigrade species, namely Bertolanius volubilis and Ramazzottius oberhaeuseri. The two species partly differ in the kind of dormant stages utilized and in habitats colonized. In both species desiccation stress did not induce an up-regulation of either Hsps. Our data, together with those from literature, suggest that in tardigrades Hsps are involved in repairing molecular damages after anhydrobiosis, rather than in the stabilization of molecules during the dry state. Finally, the first demonstration of the presence of Hsps in diapausing cysts of B. volubilis are reported and discussed.