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In the recent years many examples appeared in the literature where the configuration entropy (CE), introduced by Gleiser and Stamatopoulos, plays the role of an indicator of stability of physical systems. It was observed that, comparing states of the same system, the lower is the value of the CE, the more stable is the state. In this work we investigate the behaviour of the differential configuration entropy (DCE) , that is appropriate for systems with continuous degrees of freedom, in a new context. We consider quasi-states of quarkonium (a vector meson made of a heavy quark anti-quark pair) inside a plasma at finite density. It is known that the density increases the dissociation effect for quasi-particles inside a plasma. So, increasing the density of a thermal medium corresponds to reducing the stability of the quasi-particles. In order to investigate how this situation is translated in the Configutation Entropy context, we use a recently developed holographic AdS/QCD model for heavy vector mesons. The quasi-normal modes describing the quasi-states are obtained and the corresponding DCE is calculated. We find, for bottomonium and charmonium $1 S$ quasi-states, that the DCE increases with the quark density, or quark chemical potential, of the medium. This result shows that the DCE works again as an indicator of stability, represented in this case by the dissociation effect associated with the density.