The translocator protein (TSPO) is a 5 transmembrane mitochondrial protein involved in regulating cholesterol transport and neurosteroid synthesis. TSPO is being investigated as an in vivo brain imaging and drug treatment target as it is upregulated in neuroglia in both acute and chronic neuroinflammatory conditions including Alzheimer’s disease. Although the functional receptor form is speculated to be a dimer, the effects of pharmacological ligands on dimerisation remain largely unknown. Ligand effects on complex formation of TSPO and its missense variant, A147T, were studied using co-immunoprecipitation, FLIM-FRET and confocal microscopy of cultured cells. Co-immunoprecipitation revealed the spontaneous formation of stable dimers that was disrupted by various TSPO ligands, particularly in the presence of the A147T mutation. In addition, it was demonstrated that the deletion of the cholesterol-recognition amino acid consensus sequence at the extreme carboxyl-terminus of TSPO affects homodimerisation. Deletion of the N-terminus had no discernable effect on homodimerisation, but confocal microscopy revealed mitochondrial dysfunctions that were also reflected in gene expression changes of proteins involved in mitochondrial fission and fusion. Novel TSPO ligands were also screened for binding affinities to identify potential leads for future investigations into the effects of ligands on the TSPO dimer and for development as therapeutics