The migrant crisis in the Balkans from 2015-2016 is examined as an example of a hybrid-warfare scenario in contemporary Europe that demonstrates how institutionally-driven security responses that can be applied to successfully counter hybrid threats. Analyzing the experience of Macedonia and Bulgaria, the author identifies five types of security threats that were witnessed along the Balkan route during the migrant crisis. Migrant flows can be infiltrated by potential terrorist for the purposes of simple transit and/or attack scenarios. Organized crime, e.g. by combining human trafficking with other illegal activities, is the second security risk. Thirdly, hostile intelligence penetration of migrant inflows was a very serious hybrid threat, given the opacity of the phenomenon, i.e., the inability to distinguish ‘who is who’ and what their intentions are. Fourth, the presence of pro-migrant activist and anarchist groups with a track record of violent behavior was a persistent threat as it could be multiplied by participation of large numbers of migrants in concentrated efforts against state borders. Finally, the security situation was affected by the important, and yet often forgotten, psychological warfare.