This presentation describes the Flow cytometry data management workflow created at M.I.O (UMR 7204 CNRS, france) The objective is to manage in situ near real time flow cytometry data, and to share FCM data with scientific communityvia SeadataNet portal with metadata, Quality Codes, in interoperable formats such as ODV the software pipeline involves three steps : I) We convert complex FCM data files into a CSV readable format with numerous quality controlswith consensual vocabulary coming from BODC F02 thesaurus, and FCM large dedicated metadata ii) We insert the selected FCM data into a relational DB allowing to perform queries iii) We use Seadatanet infrastructure to make our data Findable, Accessible, Interoperable and Reusable in the Seadatanet portal This work can also be used in the Odatis national marine data infrastructure