In the SE Alps, two Cretaceous–Eocene flysch basins, Julian and Brkini, filled with turbidite sediments, are present. This study novelly reports heavy mineral assemblage counts and detrital tourmaline characterization for 11 samples. It is possible to define three different groups, characterized by the presence of (1) a clinopyroxene–epidote–low-ZTR (zircon+tourmaline+rutile; 5%) sample association, (2) a high-ZTR (>48%)–garnet–apatite association and (3) a low-ZTR (<40%)–Cr-spinel–garnet association. Detrital tourmalines from both the Julian and Brkini flysch basins are rather similar in composition, associated with metapelites and metapsammites coexisting or not coexisting with an Al-saturating phase, ferric-iron-rich quartz–tourmaline rocks and calc–silicate rocks; however, their number is drastically different. In fact, even if the percentage of heavy minerals is very low and similar in both basins (0.17–1.34% in weight), in the Julian basin, the number of tourmaline crystals is much lower than that in Brkini (1–14 vs. 30–100), suggesting an important change in the provenance area. Interestingly, the presence of a high amount of tourmaline derived from ferric-iron-rich quartz–tourmaline rocks and calc–silicate rocks makes these two basins different from all the Cretaceous flysch basins of Bosnia and the Northern Dinaric zone, where these supplies are missing or very limited.