To filter data in a MongoDB collection using PyMongo, you can use the find() method with a query parameter. The query parameter specifies the criteria for filtering data. For example, to filter documents in a collection where the value of a specific field is equal to a certain value, you can pass a dictionary with the field name and the desired value as the query parameter to the find() method. Additionally, you can use operators like $gt, $lt, $in, $nin, etc.