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Sea lamprey ( Petromyzon marinus ) and allis shad ( Alosa alosa ) have been fished for centuries in mainland Portugal during their upstream spawning migration. Here, biological information is compared for the two species and governance and monitoring data from Portugal are reviewed to propose species-specific courses of future action. Despite a national fisheries legislation common for the two species and the designation of Sites of Community Interest (SCIs) for both, the current conservation needs for sea lamprey and allis shad in Portugal are considered to be distinct. For sea lamprey, conservation priorities must focus on planning fisheries management in articulation with habitat recovery to guarantee cost-effective monitoring and sustainable long-term exploitation that adds value to local communities and pays due taxation. On the contrary, conservation concerns and actions for allis shad must strengthen and be more proactive in the reduction of fishing mortality, both target (in rivers) and bycatch (at sea). There is a need to make better use of the opportunities inherent in the Habitats Directive and the possibility to define specific management actions within SCIs. To this effect, it will be necessary to revise existing legislation and guarantee better articulation between jurisdictional authorities. A good example in this direction is the articulation already established in the river Mondego where habitat restoration, fish monitoring and effective species-specific fisheries control measures have been taken and implemented in recent years by a large institutional partnership. [ABSTRACT FROM AUTHOR]