Host ecology factors such as distributional range, behaviour and habitat differences are important in the evolution of many host-parasite systems, and these could influence the genetic structure patterns of parasites. The copepod, Caligus quadratus, parasitizes several pelagic and benthic fish species from the Southeastern Pacific coast (SEP), making this parasite a suitable model for evaluating host habit effects on the genetic patterns of generalist ectoparasites. Here, we evaluate the genetic diversity, population genetic structure, morphometric traits, and parasite fecundity among host species with different habitats and behaviour. In total, 113 specimens collected from four host fish species were sequenced using COI gen, and their morphometry and fecundity was studied. Phylogenetic analysis detected that C. quadratus from SEP is genetically different that C. quadratus from Korea. Additionally, revealed two genetics groups (two lineages), without genetic flow between them. AMOVA for each genetic group by hosts detected high gene flow among hosts. Biological traits were similar between parasite genetic groups. Neutrality tests and mismatch analyses along with the low nucleotide diversity and high haplotype diversity are characteristic of historical effects (e.g. bottleneck or founder events) followed by recent population expansion. Given that C. quadratus parasitize a wide range of hosts, it is plausible that different host selective pressures could have induced parasite reproductive mismatch due to spatially isolated (host or parasite) populations, differential mating time or failure to recognize chemical signals for mating. However, movement to the coast of migratory fish, and consequent contact with sedentary fish species, could favour the co-occurrence and persistence of both populations of parasites.