MuB, an ATP-dependent DNA-binding protein, is critical for the selection of target sites on the host chromosome during the phage Mu transposition. We developed a multichannel fluidic system to study the MuB-DNA interaction dynamics at the single DNA molecule level by total internal reflection fluorescence microscopy. We analyzed the distribution of MuB along DNA during the assembly and disassembly of MuB polymers on immobilized DNA molecules. The results reveal the absence of a significant correlation of MuB polymer distribution between the assembly and disassembly phases. These observations argue against a model in which MuB polymers on DNA represent a mixture of higher and lower affinity forms, with higher affinity forms being the first to appear and the last to disappear. Instead, assembly and disassembly of MuB polymers involve independent stochastic events. Additionally, we demonstrate that MuB disassembles from the polymer ends at a higher rate than from internal regions of the polymer and MuA stimulates MuB disassembly both at the polymer ends and internally.