The product of gene II of the distantly related, filamentous, single-stranded DNA phages IKe and Ff (M13, fd, and f1) is the only phage-encoded protein that is required for the replication of their double-stranded replicative form DNA. With the aid of recombinant plasmids containing the origins of viral strand replication [(+)-origins] of both IKe and Ff, we demonstrated that initiation but not termination of viral strand replication by gene II protein is restricted to its cognate (+)-origin. If the (+)-origins of IKe and Ff are present in the same orientation, fusion origins are generated upon gene II protein-instructed replication as a result of initiation at one origin and termination at the other. These fusion origins are only functional in the presence of the gene II protein encoded by the phage from which the sequence lying at the 3' side of the gene II protein cleavage site is derived. The nucleotides that determine the specificity of the replication initiation process are located between positions +17 and +49, or +17 and +40, with respect to the gene II protein cleavage site of IKe and Ff, respectively. The DNA sequence that forms the recognition signal for cleavage by gene II protein is probably located within the sequence that starts 3 nucleotides before and terminates 17 nucleotides after the cleavage site. Efficient packaging by phage IKe of plasmid DNA strands that contain the morphogenetic signal of Ff, or vice versa, indicates that, despite their only partial homology, the morphogenetic signals of IKe and Ff are interchangeable.