You should try the query with ObjectId
from bson.objectid import ObjectId
Document.query.get(_id=ObjectId('51e46f782b5f9411144f0efe'))
With naked pymongo
from bson.objectid import ObjectId
from pymongo import Connection
connection = Connection()
db = connection['lenin']
collection = db.document
collection.find_one({'_id': '51e35ee82e3817732b7bf3c1'}) # returns None
collection.find_one({'_id': ObjectId('51e35ee82e3817732b7bf3c1')}) # returns the object