MongoDB 2.6 supports a new $numberLong extended JSON type to represent BSON int64. There is a $undefined type that also appears to have been added in 2.6.

PyMongo's json_util module should support decoding these to the appropriate python types (None for $undefined, BSONInt64 for $numberLong).

http://docs.mongodb.org/manual/reference/mongodb-extended-json/#data_numberlong
http://docs.mongodb.org/manual/reference/mongodb-extended-json/#undefined-type

In the 2.x branch of PyMongo we'll support decoding $numberLong and $undefined, but won't introduce the new Int64 type.