Dispersal limitation, environmental selection and drift are known to influence both taxonomic similarity between communities and genetic similarity between populations. However, disentangling the relative roles of these processes on spatial patterns of differentiation—whether regarding taxonomic differentiation (TD) between communities or genetic differentiation (GD) between populations—is challenging. Investigating whether spatial patterns of TD and GD are correlated (β‐SGDCs) is a promising approach to address this issue. Here, we investigated β‐SGDCs over broad spatial scales and 22 freshwater fish species to elucidate the processes shaping TD and GD between drainage basins.