Alongside most Nigerian religious adherence were systems of belief with ancient roots in the area. These beliefs combined family ghosts with relations to the primordial spirits of a particular site. In effect the rights of a group defined by common genealogical descent were linked to a particular place and the settlements within it. The primary function of such beliefs was to provide supernatural sanctions and legitimacy to the relationship between, and the regulations governing, claims on resources, especially agricultural land and house sites. Access rights to resources, political offices, economic activities, or social relations were defined and legitimized by these same religious beliefs.
The theology expressing and protecting these relationships centered, first, on the souls of the recently dead, ghosts who continued their interest in the living as they had when they were alive. That is to say, authoritative elders demanded conformity to rules governing access to, and inheritance of, rights to resources. Indigenous theology also comprised all of the duties of the living to one another and to their customs, including their obligations to the dead ancestors whose spirits demanded adherence to the moral rules governing all human actions. The second pantheon were the supernatural residents of the land. These spirits of place (trees, rock outcroppings, a river, snakes, or other animals and objects) were discovered and placated by the original founders, who had migrated to the new site from a previous one. Spirits of the land might vary with each place or be so closely identified with a group's welfare that they were carried to a new place as part of the continuity of a group to its former home. In the new place, these spiritual migrants joined the local spirit population. Such deities developed from an original covenant created by the founders of a settlement between themselves and the local spirits. This covenant legitimized their arrival. In return for regular rites and prayers to these spirits, the founders could claim perpetual access to local resources. In doing so, they became the lineage in charge of the hereditary local priesthood and village headship and were recognized as "owners of the place" by later human arrivals. Both sets of spirits, those of family and those of place, demanded loyalty to communal virtues and to the authority of the elders in defending ancient beliefs and practices.
In addition to ensuring access to, and the continual fertility of, both land and people, the spiritual entities protected their adherents from misfortune, adjudicated disputes through trials by ordeal or through messages divined by special seers, and punished personal or communal immorality through personal and group failures, sickness, drought, fires, and other catastrophes. Special practitioners were in control of supernatural forces to heal illnesses, counter malevolent intentions by others and/or the ghostly entities, and diagnose witchcraft--the effects of malefactors whose personal spirits might cause harm, sometimes without the actual knowledge of the evildoer. Protection against misfortune was strengthened by charms, amulets, and medicinal products sold by the practitioners. In everyday life, misfortune, sickness, political rivalries, inheritance disputes, and even marital choices or the clearing of a new field could be incorporated and explained within this religious framework. Given these beliefs, causal relations were stipulated and explained through the actions of supernatural entities, whose relations to the living involved interventions that enforced morality and traditional values.
As with many peoples around the world, especially in Africa, the adult men were organized into secret societies that imitated the activity of the spirits in maintaining the moral order. In the 1980s in Igboland and in similar societies in neighboring areas, social control and conformity to moral order was still enforced by secret societies. In the 1970s, this pattern was observed spreading into small, originally autonomous communities of the southern middle belt at the northern rim of Igboland. Generally, adult men received some training and were then initiated into membership. In 1990 memberships were more selective, and in some places such organizations had died out. Specifically, these societies enforced community morality through rituals and masked dances. During these performances, secret society members imitated the spirits. They preached and expressed displeasure with and gave warnings about individual and communal morality, attributing accusations and threats to spirits of place and family who were displeased with their human charges.
Sorcery and even witchcraft beliefs persisted and were discussed as forms of medicine, or as coming from "bad people" whose spirits or souls were diagnosed as the cause of misfortune. There also were special ways in which the outcomes of stressful future activity, long trips, lingering illnesses, family and other problems could be examined. Soothsayers provided both therapy and divinatory foreknowledge in stressful situations.
In the city-states of Yorubaland and its neighbors, a more complex religion evolved that expressed the subjugation of village life within larger polities. These city-states produced a theology that linked local beliefs to a central citadel government and its sovereignty over a hinterland of villages through the monarch. The king (oba) and his ancestors were responsible for the welfare of the entire state, in return for confirmation of the legitimacy of the oba's rule over his subjects. In Oyo, for example, there were a number of national cults, each with its own priests who performed rituals under the authority of the king (alafin) in the public interest. Shango, god of thunder, symbolized the power of the king and of central government; Ogboni represented the fertility of the land and the monarch's role in ensuring the well-being of the kingdom.
In 1990 these indigenous beliefs were more or less openly practiced and adhered to among many Christians and Muslims in various parts of the country. Thus, in a number of the northern Muslim emirates, the emir led prayers for the welfare of the state at the graves of royal ancestors. In many Muslim and Christian households and villages, a number of the older religious practices and beliefs also survived. On the other hand, research indicated that many, especially younger people, believed the older traditions to be apostasy so that it was common, particularly in rural areas, to see mixtures of local beliefs with either Christianity or Islam. And in some instances, although the overall trend was away from indigenous religions and toward monotheism, older people suffered such mental and physical anguish over denouncing inherited beliefs that they abandoned the newer one.