This study aims to analyze the use Accounting Information System (AIS) on Micro to Medium Enterprises (MSMEs) of industry sectors in Manokwari. The analytical review is based on operational aspects of AIS (business size, business type, firm age, owner’s educational level and accounting knowledge) in managing MSMEs. The data of this descriptive study was collected from questionnaires and interviews given to 35 MSMEs. The result shows that the majority of MSMEs use accounting information system in its operational activities. Further, based on the operational aspects it is shown that medium enterprises, handy craft industry, business that have been operating for more than 20 years, owner’s with bachelor degree and owner’s with accounting knowledge use accounting information system more intensively. This paper can be used as a material consideration in improving the business of MSMEs in Manokwari, particularly in industry sectors.