Two closely-related earthworm species (Eisenia spp.) have long been used as model organisms in ecotoxicology. The same nanoparticles (NPs) may affect the two species differently, not only because of the inherent differences in susceptibility but also due to how the immune system could recognize NPs. In a comparative approach using E. andrei and E. fetida, we study various immune-related parameters of earthworm coelomocytes following in vitro exposure to 10 nm NPs (silver, Ag; and gold, Au) or dissolved Ag (AgNO3). In general, E. fetida coelomocytes were more susceptible to AgNPs and AgNO3 while AuNPs did not show cytotoxicity. At the sub-cellular level, AgNPs similarly affected cellular redox reactions in both species; however, E. fetida showed greater responses for apoptosis-related endpoints. At the molecular level, AgNPs (at 24 h LC20) induced a significantly high level of superoxide dismutase in E. andrei coelomocytes while E. fetida was additionally characterized by consistent induction of metallothionein and differential capacity for redox/metal regulation. Although AuNPs were not cytotoxic, both NP types (Ag and Au) seemed to alter the expression pattern of immune-related genes (toll-like receptor and lysenin) in both species, but more clearly in E. fetida. We further observed that lysenin proteins, while secreted differentially between the two species, bind only to AgNPs resulting in negative secretion feedback. Our findings support the general preference for E. fetida in ecotoxicology, and reveal the potential roles of protective and immune mechanisms optimized for each species in its own ecological niche.