Druglike small molecules with photoswitchable bioactivity—photopharmaceuticals—allow biologists to perform studies with exquisitely precise and reversible, spatial and temporal control over critical biological systems inaccessible to genetic manipulation. The photoresponsive pharmacophores disclosed have been almost exclusively azobenzenes, which has limited the structural and substituent scope of photopharmacology. More detrimentally, for azobenzene reagents, it is not researchers’ needs for adapted experimental tools, but rather protein binding site sterics, that typically force whether the trans (dark) or cis (lit) isomer is the more bioactive. We now present the rational design of HOTubs, the first hemithioindigo‐based pharmacophores enabling photoswitchable control over endogenous biological activity in cellulo. HOTubs optically control microtubule depolymerisation and cell death in unmodified mammalian cells. Notably, we show how the asymmetry of hemithioindigos allows a priori design of either Z‐ or E‐ (dark‐ or lit)‐toxic antimitotics, whereas the corresponding azobenzenes are exclusively lit‐toxic. We thus demonstrate that hemithioindigos enable an important expansion of the substituent and design scope of photopharmacological interventions for biological systems. Switch me off, switch me on: The first use of the hemithioindigo scaffold as a photoswitchable inhibitor pharmacophore is reported for the preparation of photopharmaceuticals to control endogenous cytoskeleton structure and cell cycle. Hemithioindigos allow a priori design of either Z‐ or E‐ (dark‐ or lit‐) bioactives, so they may address the problem of undesirable dark activity in the chemistry of cellular photopharmaceuticals.