Living in this globalization era, makes all the transactions became instant and fast. As an archipelago country, Indonesia has a deep connection with the airline companies as its transportation tool. Nowadays, we purchase an airline ticket through internet connection that is run by computer program. This Computer program has become an object of intellectual property protection. This research is done to find the problem of the legal uncertainty between patent and copyright protections and to know the legal certainty of those protections. Garuda has had a copyright protection for their online ticketing system and they registered it to the copyright office. However, Bagus Tanuwidjaja registered a patent application for the same object which was the online ticketing system. Furthermore, it has been granted for patent protection by patent examiner. This action has raised a wrongful implementation in which making a divergence copyright understanding, and creating confusion to the intellectual property world. Law No. 19 of 2002 on Copyright is stipulated that a computer program is an object in copyright protection. Bagus Tanuwidjaja invention’s has not been fulfilled the main requirements from the patent registration. The main requirements are novelty, inventive steps, and industrial applicable. Online ticketing system has a source code and object code as a programming language. Copyright will give protection for those codes for getting the copyright protection, in which is stipulated in Indonesian’s Copyright Law. Therefore, Garuda sent a lawsuit to Bagus Tanuwidjaja to the Commercial Court to restore their right back, and to find who is the right holders in this invention. As a holders of judicative authority, Commercial Court and Supreme Court will make a verdict that will be settle this dispute