Since the discovery of the integration mechanism of the filamentous phage CTXϕ of Vibrio cholerae, integrating filamentous phages have been discovered to be more abundant and diverse than previously recognized. However, the integration systems of filamentous phages have not been fully investigated. The present review provides a short overview on the different strategies employed by filamentous bacteriophages for integration into the host chromosome. This is the first review to describe the diversity of site-specific recombination in filamentous phages.