The sea louse (Caligus rogercresseyi) is the most significant parasitic pathogen in Chilean salmon farms, and it infects farmed salmon and native host fish. Fecundity is one of the most important parameters for understanding the population dynamics of a species; however, this information is scarce for this parasite. The fecundity of C. rogercresseyi females collected from native hosts (Eleginops maclovinus) captured near salmon farms in southern Chile was measured to evaluate the reproductive output of this parasite on this host fish. From June 2008 to May 2009, 212 specimens of E. maclovinus were examined. Each fish was measured, and all its parasites were collected, sorted and counted. Seventy-nine ovigerous C. rogercresseyi females (OFs) were measured. Total body length, egg string length and total number of eggs per string were recorded for each parasite. Ovigerous females body length varied between 3.9 and 5.0 mm. Fecundity varied between 12 and 56 eggs string-1, and it was correlated with OF body length. Temporal variations in OF fecundity were explained by co-variation in OF body length, but not by month. Ovigerous females on E. maclovinus were smaller and showed lower fecundity than OFs on farmed salmon. Our results suggest that native hosts play a secondary role in C. rogercresseyi egg production in Codigue bay.