The binding interaction of surfactant cobalt(III) complex, cis-[Co(bpy)2(HA)2](ClO4)3, in which bpy is 2,2-bipyridine and HA is hexadecylamine or cetylamnine with DNA was through intercalative mode via the long aliphatic chains present in the ligands. The binding was investigated by various techniques, electronic absorption, fluorescence spectroscopy, circular dichroism (CD), cyclic voltametry (CV) and viscosimetry measurements. The spectroscopic studies together with cyclic voltammetry and viscosity experiments support that the surfactant cobalt(III) complex binds to calf thymus DNA by intercalation through the aliphatic chain present in the complex into the base pairs of DNA. The presence of bipyridine ligand with larger π-frame work may also enhance intercalation. UV–vis., spectrum showed 4 nm bathochromic shift of the absorption band at 352 nm along with significant hypochromicity for the absorption band of the complex. The intrinsic binding constants(at below and above CMC are Kb = 2.41 × 105M−1, Kb = 3.12 × 106M−1 respectively) is more in keeping with intercalators and suggests this binding mode. The viscosity measurements showed that the surfactant cobalt(III) complex-DNA interaction can be hydrophobic and confirm intercalation. Moreover, the complex induced detectable changes in the CD spectrum of CT-DNA. Competitive binding study with ethidium bromide (EB) shows that the surfactant complex exhibits the ability to displace the DNA-bound EB indicating that the complex binds to DNA in strong competition with EB for the intercalative binding site. Also, CV results confirm this mode because, with increasing the CT-DNA concentration, shift to higher potential was observed. Besides the effect of binding of surfactant cobalt(III) complex to DNA in presence of β-cyclodextrin has also studied. This binding of the surfactant cobalt(III) complex in presence of β-cyclodextrin medium has been prevented (at below and above CMC are Kb = 5.45 × 104M−1, Kb = 6.92 × 105M−1 respectively) due to the incorporation of the aliphatic chains into the cavity of β-cyclodextrin. In presence of β-cyclodextrin the binding occur through surface and (or) groove binding can be attributed to the inclusion of the long aliphatic chain that is present in one of the ligands into cyclodextrin.