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What are the connections between civil conflict fought between insurgency and the state, and inter-group conflicts fought between non-state armed actors? As we see in the examples of Bosnian and Sudanese civil war, countries that experience civil war are confronted with internal conflicts that occur sub-nationally between social groups at the communal level composed of non-state armed actors, often organized along ethnic identity groups (e.g. Muslims against Muslims). To answer this question, I identify three causal pathways that explain inter-connection of violence that appear between Muslim clan groups, and violence involving insurgency and the state army. Using a single case on Mindanao conflict in the southern Philippines, I test existing theories on civil war and conflict that hypothesize mechanisms of inter-linkages between civil war and communal conflicts. I then present three theories of inter-connection derived inductively by examining empirical cases of communal violence, and tracing the processes of communal violence. The three hypothesized theories of inter-connection can be explained by a) direct involvement of insurgency members into communal violence, b) the inter-linking agent role of political elites and paramilitaries as guns-for-hire, and c) informal communal conflict resolution mechanism involving insurgency as the intermediary. The three hypothesized mechanisms contribute to the existing theories of conflict and violence by empirically demonstrating micro-level processes of violence that develop as a result of repeated social interactions between conflict actors at the communal and state-level.