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Space types are used to define common characteristics (internal loads, schedules, OA requirements, infiltration, construction). If you have lots of office rooms in your model, you would create one "Office Space Type" to assign to each of these rooms. In OpenStudio, each of those rooms is called a "Space".

Thermal zones are used to define a volume that is served by an HVAC system. If a terminal serves multiple rooms, then you will want to assign each of the corresponding Spaces in your OpenStudio model to one thermal zone. Thermal zones can have multiple spaces, but spaces cannot have multiple thermal zones. If you have a very large space like a gym served by multiple terminals, then to accurately model air supply effects you could split the large space into multiple spaces, one for each terminal.

NOTE: if you draw a space and do not assign it to a thermal zone, OpenStudio WILL NOT convert it into an EnergyPlus zone (you'll see a gaping hole in your final IDF that OpenStudio produces). If you have unconditioned spaces, you should create an "Unconditioned" thermal zone that doesn't have any HVAC connections.