A method of identifying hydrocarbon seeps that are connected to hydrocarbon reservoirs and for identifying in situ conditions of hydrocarbon reservoirs is disclosed. The method comprises, obtaining a sample from an area of interest, such as a sediment sample or water column sample near a hydrocarbon seep; analyzing the sample to detect microbial signatures that are specific to families associated with hydrocarbon reservoirs; and using the signature to determine whether the hydrocarbon seep is connected to a hydrocarbon reservoir and to identify properties of the hydrocarbon reservoir.