Entering big data era, individual GPS trajectory data has created great opportunities for human mobility and collective behavior studies. Individual GPS trajectories can be collected by location-based services on mobile phones. However, GPS data often do not record transportation modes (e.g., walking, riding a bus, or driving a car). In this study, we analyzed the statistical characteristics of individual trajectories and present a collaborative isolation forest (Co-IF) model to identify the transportation modes of mobile phone GPS trajectories. Unlike previous models that identify multiple transportation modes simultaneously, the proposed Co-IF model builds a single-class classifier for each transportation mode and then combines their results. Compared to existing models, the Co-IF model offers competitive performance and shows improved reliability with noisy trajectories.