MySQL and MongoDB are both free and open source databases. MySQL and MongoDB have a lot of basic differences in terms of data representation, querying, relationships, transactions, schema design and definition, normalization, speed and performance. By comparing MySQL with MongoDB, we are comparing Relational and non-relational databases. MongoDB is a scalable and high-performance open source database designed to handle document-oriented storage while MySQL is a widely used relational database. When building a custom web application, you need to consider the type of database that best suits your demand. If your are thinking to go with the best open source database, you will have to consider which database is best for you: MySQL or MongoDB? Here's a quick guide on the basic differences between MySQL (Relational) and MongoDB (Non-Relational / NoSQL).