We present a novel mixture of trees (MoT) graphical model for video segmentation. Each component in this mixture represents a tree structured temporal linkage between super-pixels from the first to the last frame of a video sequence. Our time-series model explicitly captures the uncertainty in temporal linkage between adjacent frames which improves segmentation accuracy. We provide a variational inference scheme for this model to estimate super-pixel labels and their confidences in nearly realtime. The efficacy of our approach is demonstrated via quantitative comparisons on the challenging SegTrack joint segmentation and tracking dataset.