Methylmercury (MeHg) is a potent neurotoxin that biomagnifies in marine food webs. Inorganicmercury (Hg) methylation is conducted by heterotrophic bacteria inhabiting sedimentor settling detritus, but endogenous methylation by the gut microbiome of animals in thelower food webs is another possible source. We examined the occurrence of the bacterialgene (hgcA), required for Hg methylation, in the guts of dominant zooplankters in the NorthernBaltic Sea. A qPCR assay targeting the hgcA sequence in three main clades (Deltaproteobacteria,Firmicutes and Archaea) was used in the field-collected specimens ofcopepods (Acartia bifilosa, Eurytemora affinis, Pseudocalanus acuspes and Limnocalanusmacrurus) and cladocerans (Bosmina coregoni maritima and Cercopagis pengoi). All copepodswere found to carry hgcA genes in their gut microbiome, whereas no amplification wasrecorded in the cladocerans. In the copepods, hgcA genes belonging to only Deltaproteobacteriaand Firmicutes were detected. These findings suggest a possibility that endogenousHg methylation occurs in zooplankton and may contribute to seasonal, spatial andvertical MeHg variability in the water column and food webs. Additional molecular and metagenomicsstudies are needed to identify bacteria carrying hgcA genes and improve theirquantification in microbiota.