Microbiomes of the neritic copepod species Acartia tonsa and Temora longicornis collected in coastal Danish waters were investigated by use of 16S rRNA gene-Amplicon highthroughput sequencing. In contrast to current assumptions and findings, microbiomes of the 2 copepod species from the same environment were significantly different in bacterial species composition, particularly in terms of relative abundance of bacteria associated with each copepod species. The microbiomes of both species, likewise, differed from that of A. tonsa reared in laboratory culture, but similarities were also observed between wild and laboratory-reared A. tonsa. Alpha proteobacteria dominated A. tonsa microbiomes, whereas Gammaproteobacteria were most abundant in T. longicornis microbiomes. The overall diversity of bacteria associated with the 2 copepod species was to some extent in harmony with previous findings, but several of the most abundant operational taxonomic units correspond to bacteria that have not previously been found in association with marine copepods. The results thus add to the knowledge of the diversity of microbiomes of marine zooplankton organisms and document the fact that different planktonic copepod species from the exact same environment may host significantly different microbiomes. Hence, different copepod species are either not colonized by the same bacteria assemblages or support colonization/growth of different bacteria populations, leading to distinct copepod microbiomes.