Dispersal is a fundamental and crucial ecological process for a metapopulation to survive in heterogeneous or changing habitats. In this paper, we investigate the effect of the habitat quality and the dispersal on the neutral genetics diversity of a metapopulation. We model the metapopulation dynamics on heterogeneous habitats using a deterministic system of ordinary differential equations. We decompose the metapopulation into several neutral genetic fractions seeing as they could be located in different habitats. By using a mathematical model which describes their temporal dynamics inside the metapopulation, we provide the analytical results of their transient dynamics, as well as their asymptotic proportion in the different habitats. The diversity indices show how the genetic diversity at a global metapopulation scale is preserved by the correlation of two factors: the dispersal of the population, as well as the existence of adequate and sufficiently large habitats. The diversity indices show how the genetic diversity at a global metapopulation scale is preserved by the correlation of two factors: the dispersal of the population as well as the existence of adequate and sufficiently large habitats. Moreover, they ensure genetic diversity at the local habitat scale. In a source-sink metapopulation, we demonstrate that the diversity of the sink can be rescued if the condition of the sink is not too deteriorated and the migration from the source is larger than the migration from the sink. Furthermore, our study provides an analytical insight on the dynamics of the solutions of the systems of ordinary differential equations.