Abstract: Research on the differences of organizational effectiveness of Sapordanco village and Bonkawir village in Waisai City of Raja Ampat regency is done by taking entire apparatus in both villages (total sample) as respondents. The comparative approach is used to analyze the differences between the two villages as the lowest government organizations that play a role in people’s interests as they are close to the people. It can be studied from functions or dimensions such as leadership, coordination, morale, motivation, efficiency level, satisfaction, structure, communication and management. The results of analysis of all functions or dimensions show that there are differences between the two villages in improving the effectiveness of the functions or dimensions. These differences contribute differently to the level of organizational effectiveness in each village. The results of the analysis show that Sapordanco village is more effective than Bonkawir village. There are differences between the two villages; all Sapordanco village apparatus are committed to perform governmental tasks, services and development in accordance with maximization of main tasks and functions because the village lies downtown while Bonkawir village apparatus have lower discipline level because the location of the village is far from downtown.