The pocilloporin Rtms5 and an engineered variant Rtms5^H146S undergo distinct color transitions (from blue to red to yellow to colorless) in a pH-dependent manner. pK_a values of 4.1 and 3.2 were determined for the blue (absorption λ_max, 590 nm) to yellow (absorption λ_max, ∼453 nm) transitions of Rtms5 and Rtms5^H146. The pK_a for the blue-yellow transition of Rtms5^H146S increased by 1.4 U in the presence of 0.1 M KI, whereas the pK_a for the same transition of Rtms5 was relatively insensitive to added halides. To understand the structural basis for these observations, we have determined to 2.0 Å resolution the crystal structure of a yellow form of Rtms5^H146S at pH 3.5 in the presence of iodide. Iodide was found occupying a pocket in the structure with a pH of 3.5, forming van der Waals contacts with the tyrosyl moiety of the chromophore. Elsewhere, it was determined that this pocket is occupied by a water molecule in the Rtms5^H146S structure (pH 8.0) and by the side chain of histidine 146 in the wild-type Rtms5 structure. Collectively, our data provide an explanation for the observed linkage between color transitions for Rtms5^H146S and binding to halides.