We study a meson mass splitting due to isospin violation in holographic dense matter. We work in a D4/D6/D6 model with two quark flavor branes to consider asymmetric dense matter in holographic QCD. We mainly consider two cases. We first consider $m^+/m^-sim m_d/m_u$ to study the effect of isospin violation on the meson masses. Then, we take $m^+/m^-sim m_s/m_q$, where $m_qsim(m_u+m_d)/2$, to calculate in-medium kaon-like meson masses. In both cases we observe that the mass splitting of charged mesons occurs at low densities due to the asymmetry, while at high densities their masses become degenerate. At intermediate densities, we find an exotic behavior in masses which could be partly understood in a simple picture based on the Pauli exclusion principle.
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