The Argentine attacker has taken to Facebook and stated that his team will have a job on their hands against the Bavarians.
The fixtures will pit former Blaugrana favourite Pep Guardiola against the Catalan giants, with the winner set to face either Real Madrid or Juventus in the final.
Lionel Messi reacted to the draw by posting on Facebook, stating that the games against the current Bundesliga holders would be incredibly tough.
Messi will feature against his former mentor Guardiola for the first time since the Spanish manager left Camp Nou in 2012.
The four-times Ballon d’Or winner has been in incredible form since the turn of the year, scoring goals and creating assists with alarming regularity.
Barcelona are still in contention for a memorable treble under Luis Enrique this season, with the Camp Nou side still able to win La Liga, the Copa del Rey and the Champions League.
Messi played a part in helping Barca dispose of Paris Saint-Germain in the last round, with Enrique’s men looking like Europe’s top team at the moment.