During 12–14 March 2018, researchers from Argentina, Bolivia, Brazil, and Paraguay met in Asuncion, Paraguay for the workshop Developing a transboundary monitoring framework for the jaguar (Panthera onca) in the Southern Cone towards determining transboundary research needs for jaguar in these four countries. We defined a focal area of interest, which includes 15 Jaguar Conservation Units JCUs and seven ecoregions. For this focal area we defined research needs to determine population status and viability, connectivity, and genetic diversity among units, as well as connectivity with the continental core populations in the Amazon. We prioritized conducting research outside of protected areas, particularly in areas dominated by row crops and grazing. Furthermore, we identified a need for increased research on the movement of individuals and genes through the landscape to be incorporated into the assessment of population connectivity. Also, the intentional killing of jaguars needs to be better quantified, including research on the human dimensions of killing, as mortality is high in many areas and limits jaguar occurrence despite the availability of suitable habitat.