Green fluorescent protein (GFP) is widely used as a biomarker in living systems, however GFP and its variants are prone to forming low-affinity dimers under physiological conditions. This undesirable tendency is exacerbated when fluorescent proteins (FP) are confined to membranes fused to naturally-oligomeric proteins or expressed at high levels in cells. Oligomerization of FPs introduces artifacts into the measurement of subunit stoichiometry as well as interactions between proteins fused to FPs. Introduction of a single mutation A206K has been shown to disrupt hydrophobic interactions in the region responsible for GFP dimerization thereby contributing to its monomerization. Nevertheless a detailed understanding of how this single amino acid-dependent inhibition of dimerization in GFP occurs at the atomic level is still lacking. Single-molecule experiments combined with computational microscopy (atomistic molecular dynamics) revealed that the amino group of A206 contributes to GFP dimer formation via a multivalent electrostatic interaction. We further showed that myristoyl modification is an efficient mechanism to promote membrane attachment of GFP. Molecular dynamics-based site-directed mutagenesis has been used to identify the key functional residues in FPs. The data presented here have been utilized as a monomeric control in downstream single-molecule studies facilitating more accurate stoichiometry quantification of functional protein complexes in living cells.