A system and method is provided for generating and using multiple synchronized local program timestamps in a media processing system. The system includes an input processor, one or more local timestamp insertion modules, one or more parsers, and an input buffer. Each local program timestamp module includes a clock reference recovery module, a local program clock synchronized to the system time clock of a program source, and a timestamp generator. The system also includes one or more processing modules such as record modules, transmission modules, and display modules. When a data packet is received by the media processing system, the local timestamp insertion module appends a timestamp to the data packet. The timestamp is based on the synchronized local program clock for the program associated with the data packet. The processing modules utilize the synchronized local timestamps and their associated local program clock in a variety of applications.