Humic substances (HS) are ubiquitous biogeochemicals and major constituents of all surface waters. HS are internalised by exposed organisms which, in turn, respond with anti-stress reactions. However, the outcome of these reactions is not necessarily negative; rather, it can lead to increases in individual lifespan and lifetime reproductive output. If clones of two closely related species respond differently, HS have the potential to shape the community structure. We obtained clones of Moina macrocopa and Moina micrura from Brazilian habitats and this potential to affect the community structure was tested with HuminFeed ® (HF), a commercial HS preparation exotic to the animals, and with regional HS from a Brazilian coastal lagoon. Upon exposure to HF, the M. macrocopa clone responded with only a slight increase in lifespan and reproductive output. However, when exposed to the Brazilian HS, a strong lifespan extension and a reduction in lifetime reproductive output occurred in this clone. Upon exposure to HF, the M. micrura clone responded with a reduced lifespan and reproductive output. Upon exposure to HS, none of the Moina clones showed a delay in the onset of reproduction. Our results show that HF impacts the clones of two sister Moina species differently, and hence has the potential to shape zooplankton communities.