This paper will describe the day-to-day control of the Measurements Of Pollution In The Troposphere (MOPITT) instrument. The MOPITT onboard software is designed to make maintenance of the instrument fairly simple in nature. Very few commands are required during normal operations, and the instrument, once set up, can be run for several months with no additional intervention. The ground system that controls the Terra spacecraft, of which MOPITT is one instrument, allows both real time commanding and scheduled commanding. The scheduled commanding can be planned far in advance and uses pre-tested blocks of command sequences to do more complicated instrument functions, such as long calibration events. MOPITT commands are arranged in a hierarchy that allows "top level" routine commanding to be carried out efficiently, but also permits "bottom level" commanding to deal with unforeseen conditions. The extensive use of tables, and the ability to update the permanent memory on-orbit, all contribute to a simple yet powerful, control capability. Real time commanding is directed by MOPITT IOT (Instrument Operations Team) members at the University of Toronto (UoT) on a voice line that is permanently connected to the Earth Observing System (EOS) Operations Center (EOC) in Greenbelt, Maryland. A data link permits real-time displays of the instrument status to be viewed by the Toronto personnel. EOC personnel send instrument commands after confirmation from UoT personnel. This method of operation is extremely reliable and has been used extensively to do routine maintenance and configuration changes of the MOPITT instrument.