Herein, we report the synthesis of silver nanoparticles (AgNPs) using direct micelles and reverse micelles of sodium bis (2-ethylhexyl) sulfosuccinate (AOT) as reaction media. We evaluated the effect of these self-organized aggregates in the nucleation and growth mechanism of AgNPs. The results show the effect of water when it is a confined medium, where their properties are different from those of net water. These factors strongly influence the size, polydispersity and shape of nanoparticles. Moreover, the presence of ions from the reducing agents and the surfactant, it is a key factor in the anisotropy of the AgNPs obtained. For our knowledge, this is the first report in which the effect of the reaction media is evaluated by using direct and reverse micelles to synthesize silver nanoparticles. Additionally, AgNPs synthesized through the two systems were functionalized with folic acid and evaluated their cytotoxicity and photothermal properties. The results show that AgNPs synthesized through the two systems are potential photothermal agents, reaching to reduce up to 47% of the viability of the HeLa cells, using a laser of 808 nm.