An example method of identifying a hybrid connection associated with a network flow in a multi-cloud computing system includes: obtaining, by a network analyzer, network information from a plurality of data centers in the multi-cloud computing system, the plurality of data centers corresponding to a respective plurality of namespaces; identifying Internet Protocol (IP) subnetworks associated with the hybrid connection from the network information; generating connection indexes for the namespaces relating source IP subnetworks of the IP subnetworks, destination IP subnetworks of the IP subnetworks, and an identifier for the hybrid connection; searching a source IP address and a destination IP address of a flow record for the network flow in the connection indexes to obtain the identifier for the hybrid connection; and tagging the flow record with the identifier for the hybrid connection.