Photochromic switches and genetically encoded biosensors have become powerful tools for monitoring and modulating the activity of neurons and neuronal networks. Our understanding of the mechanisms underlying the development and functioning of the nervous system has greatly advanced in recent years thanks to advancements in these effective molecular and genetic tools. The idea of this Special Research Issue of Frontiers in Molecular Neuroscience is to provide an overview of the approaches in this area of research, and to present new applications in molecular imaging of ions and remote activation of receptors, ionic channels and synaptic networks. The issue contains experimental and methodological papers as well as review articles dealing with molecular tools for investigation and modulation of neuronal function. It can be divided into two main sections: (i) genetically encoded probes for non-invasive monitoring of ions and ATP; and (ii) optogenetic and optopharmacologic tools for control of neuronal activity with light.