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We compute the thermal free energy in large N U(N) Chern-Simons-matter theories with matter fields (scalars and/or fermions) in the fundamental representation, in the large temperature limit. We note that in these theories the eigenvalue distribution of the holonomy of the gauge field along the thermal circle does not localize even at very high temperatures, and this affects the computation significantly. We verify that our results are consistent with the conjectured dualities between Chern-Simons-matter theories with scalar fields and with fermion fields, as well as with the strong-weak coupling duality of the N=2 supersymmetric Chern-Simons-matter theory.

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