Optogenetics and photopharmacology are two perspective modern methodologies for control and monitoring of biological processes from an isolated cell to complex cell assemblies and organisms. Both methodologies use optically active components that being introduced into the cells of interest allow for optical control or monitoring of different cellular processes. In optogenetics, genetic materials are introduced into the cells to express light-sensitive proteins or protein constructs. In photopharmacology, photochromic compounds are delivered into a cell directly but not produced inside the cell from a genetic material. The development of both optogenetics and photopharmacology is inseparable from the design of improved tools (protein constructs or organic molecules) optimized for specific applications. Herein, we review the main tools that are used in modern optogenetics and photopharmaclogy and describe the types of cellular processes that can be controlled by these tools. Although a large number of different kinds of optogenetic tools exist, their performance can be evaluated with a limited number of metrics that have to be optimized for specific applications. We classify these metrics and describe the ways of their improvement.