Understanding how individual behavior shapes the structure and ecology of populations is key to species conservation and management. Like many elasmobranchs, manta rays are highly mobile and wide-ranging species threatened by anthropogenic impacts. In shallow water environments, these pelagic rays often form groups and perform several apparently socially mediated behaviors. Group structures may result from active choices of individual rays to interact or passive processes. Social behavior is known to affect spatial ecology in other elasmobranchs, but this is the first study providing quantitative evidence for structured social relationships in manta rays. To construct social networks, we collected data from more than 500 groups of reef manta rays (Mobula alfredi) over 5 years in the Raja Ampat Regency of West Papua. We used generalized affiliation indices to isolate social preferences from non-social associations, the first study on elasmobranchs to use this method. Longer lasting social preferences were detected mostly between female rays. We detected assortment of social relations by phenotype and variation in social strategies, with the overall social network divided into two main communities. Overall network structure was characteristic of a dynamic fission-fusion society, with differentiated relationships linked to strong fidelity to cleaning station sites. Our results suggest that fine-scale conservation measures will be useful in protecting social groups of M. alfredi in their natural habitats and that a more complete understanding of the social nature of manta rays will help predict population responses to anthropogenic pressures, such as increasing disturbance from dive tourism.