Understanding of mercury (Hg) complexation with low molecular weight (LMW) bioligands will help elucidate its speciation. In natural waters, the rate of this complexation is governed by physicochemical, geochemical and biochemical parameters. However, the role of bioligands involved in Hg intracellular handling by aquatic microorganisms is not well documented. Here, we combine the use of isotopically-labelled Hg species (inorganic and monomethyl mercury, iHg & MeHg) with hyphenated techniques based on gas or liquid chromatography coupling to elemental and molecular mass spectrometry to explore the role of intracellular biogenic ligands involved in iHg and MeHg speciation in cyanobacterium Synechocystis sp. PCC 6803, a representative phytoplankton species. The experiment was carried out at low Hg concentration (3 nM / 600 ng L-1 199iHg & 0.3 nM / 60 ng L-1 Me201Hg), one of the lowest reported so far for Hg species incubation with photosynthetic unicellular organisms. This approach allowed us to track resulting metabolic and newly-found intracellular Hg biocomplexes (e.g. organic thiols) in Synechocystis sp. PCC 6803. In the cytosolic fraction, we found different Hg species binding affinities with both high and low molecular weight (HMW & LMW) bioligands after 5 minutes and 24 hours of Hg exposure in the exponential and stationary phase. Furthermore, the parallel detection with both elemental and molecular ionization sources allowed the sensitive detection and molecular identification of glutathione (GSH) as the main low molecular weight binding ligand to iHg ((GS)2-Hg) and MeHg (GS-MeHg) in the cytosolic fraction. Such novel experimental approach expands our knowledge on the role of biogenic ligands involved in iHg and MeHg intracellular handling in cyanobacterium.