The Internet of Things (IoT) introduces a new challenge for Database Management Systems (DBMS). In IoT, large numbers of sensors are used in daily lives. These sensors generate a huge amount of heterogeneous data that needs to be handled by the appropriate DBMS. The IoT has a challenge for the DBMS in evaluating how to store and manipulate a huge amount of heterogeneous data. DBMS can be categorized into two main types: The Relational DBMSs and the Non-relational DBMSs. This paper aims to provide a thorough comparative evaluation of two popular open-source DBMSs: MySQL as a Relational DBMS and MongoDB as a Non-relational DBMS. This comparison is based on evaluating the performance of inserting and retrieving a huge amount of IoT data and evaluating the performance of the two types of databases to work on resources with different specifications in cloud computing. This paper also proposes two prediction models and differentiates between them to estimate the response time in terms of the size of the database and the specifications of the cloud instance. These models help to select the appropriate DBMS to manage and store a certain size of data on an instance with particular specifications based on the estimated response time. The results indicate that MongoDB outperforms MySQL in terms of latency and the database size through increasing the amount of tested data. Moreover, MongoDB can save resources better than MySQL that needs resources with high capabilities to work with less performance.