You can query using the bson.binary.Binary type. Here's an example using a UUID (kinda contrived since PyMongo supports UUIDs natively as well):
>>> from uuid import uuid4, UUID
>>> u = uuid4()
>>> u.bytes
'z\x0e\x0f\x18\xce\x83OW\xa5\xd6\xb8\xbd\x00#\x0c\xa5'
>>>
>>> from bson.binary import Binary
>>> c.test.bin.insert({'bin': Binary(u.bytes, 128)})
ObjectId('50c7ce8ffba52232239f7f6d')
>>> c.test.bin.find({'bin': Binary('z\x0e\x0f\x18\xce\x83OW\xa5\xd6\xb8\xbd\x00#\x0c\xa5', 128)}).count()
1
>>> list(c.test.bin.find({'bin': Binary('z\x0e\x0f\x18\xce\x83OW\xa5\xd6\xb8\xbd\x00#\x0c\xa5', 128)}))
[{u'bin': Binary('z\x0e\x0f\x18\xce\x83OW\xa5\xd6\xb8\xbd\x00#\x0c\xa5', 128), u'_id': ObjectId('50c7ce8ffba52232239f7f6d')}]