We study the holographic light meson spectra and their mass splitting in the nuclear medium. In order to describe the nuclear matter, we take into account the thermal charged AdS geometry with two flavor charges, which can be reinterpreted as the number densities of proton and neutron after some field redefinitions. We show that the meson mass splitting occurs when there exists the density difference between proton and neutron. Depending on the flavor charge, the mass of the positively (negatively) charged meson increases (decreases) as the density difference increases, whereas the neutral meson mass is independent of the density difference. In the regime of the large nucleon density with a relatively large number difference between proton and neutron, we find that negatively charged pion becomes massless in the nuclear medium, so the pion condensate can occur. We also investigate the binding energy of a heavy quarkonium in the nuclear medium, in which the binding energy of a heavy quarkonium becomes weaker as the density difference increases.
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