In order to better understand the origin and enrichment mechanisms leading to elevated Zn concentrations in Jurassic limestone of the Jura mountain range (JMR) and the Burgundy (B), we investigated four locations of Bajocian age (JMR: Lausen-Schleifenberg, Gurnigel; B: Vergisson-Davayé, Lucy-le-Bois) and two locations of Oxfordian age (JMR: Dornach, Pichoux) for their Zn distribution and speciation. Measurements of the acid-extractable and bulk Zn contents showed that Zn is stratigraphically and spatially heterogeneously distributed, in association with permeable carbonate levels. Up to 3,580 and 207 mg/kg Zn was detected in Bajocian and Oxfordian limestone, respectively, with numerous limestone samples having Zn contents above 50 mg/kg. Using X-ray absorption near edge structure spectroscopy and micro-X-ray fluorescence spectrometry, the speciation and microscale distribution of Zn was investigated for selected limestone samples. In Bajocian limestone sphalerite and/or Zn-substituted goethite and a minor fraction of Zn-bearing carbonates were identified. In contrast, Zn-bearing carbonates (Zn-substituted calcite and hydrozincite) were accounting for most of the total Zn in Oxfordian limestone. The micro-scale distribution of Zn for Bajocian and Oxfordian limestone was however similar with localized Zn-rich zones in the limestone cement and at the rim of oolites. The stratigraphic sporadicity and microscale heterogeneity of the Zn distribution together with the Zn speciation results point to a hydrothermal origin of Zn. Occurence of Zn-goethite is probably linked to the oxidative transformation of framboidal pyrite and hydrothermal sphalerite in contact with meteoritic waters. Difference in speciation between Bajocian limestone and Oxfordian limestone may be related to differences in rock permeability Geosci (2011) 104:409-424 DOI 10.1007 and/or to various hydrothermal events. Isotopic dating of the different mineralizations will be needed to decipher differences in Zn speciation and the precise chronology of hydrothermal episodes.