A series of partially fluorinated (C6F13H-modified) polystyrene-b-1,2-polybutadiene (PS-b-1,2-PB) copolymers were prepared by the reaction of a model PS-b-1,2-PB copolymer with n-C6F13I followed by substitution of hydrogen for the iodine by hydrogenolysis. The morphologies and domain spacings of the ordered samples at 120 and 195 degreesC were determined as a function Of C6F13H modification extent using small-angle X-ray scattering (SAXS). From the domain spacings an effective interaction parameter (chi(eff)) between the PS and partially C6F13H-modified 1,2-PB blocks was estimated. The chi(eff) at 120 degreesC increases significantly with fluorination, from ca. 0.05 (0 mol % C6F13H modification) to ca. 0.75 (80 mol % C6F13H modification). The order-disorder transition temperature (T-ODT) for a partially C6F13H-modified PS-b-1,2-PB (25 mol %) was determined to be 186 +/- 3 degreesC, using rheology and static birefringence. From self-consistent mean-field theory chi(eff) for this block copolymer is estimated to be 0.16 at T-ODT, which agrees well with the value of 0.21 estimated from the domain spacing. These estimated interaction parameters demonstrate that a selective perfluoroalkylation approach can strongly enhance the incompatibility of PS-b-1,2-PB copolymers and is a powerful method for examining large regions of the block copolymer phase diagram with a single precursor molecule.