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Members of groups 1 (e.g. ϕ29) and 2 (e.g. Nf) of the ϕ29 family of phages infect the spore forming bacterium Bacillus subtilis. Although classified as lytic phages, the lytic cycle of ϕ29 can be suppressed and its genome can become entrapped into the B. subtilis spore. This constitutes an alternative infection strategy that depends on the presence of binding sites for the host-encoded protein Spo0A in the ϕ29 genome. Binding of Spo0A to these sites represses ϕ29 transcription and prevents initiation of DNA replication. Although the Nf genome can also become trapped into B. subtilis spores, in vivo studies showed that its lytic cycle is less susceptible to spo0A-mediated suppression than that of ϕ29. Here we have analysed the molecular mechanism underlying this difference showing that Spo0A differently affects transcription and replication initiation of the genomes of these phages. Thus, whereas Spo0A represses all three main early promoters of ϕ29, it only represses one out of the three equivalent early promoters of Nf. In addition, contrary to ϕ29, Spo0A does not prevent the in vitro initiation of Nf DNA replication. Altogether, the differences in Spo0A-mediated regulation of transcription and replication between ϕ29 and Nf explain their different behaviours in vivo., Spanish Ministry of Education and Science (BFU2005-00733 to M.S., BFU2005-01878 to W.J.J.M.); Spanish Ministry of Science and Innovation (BFU2008-00215/BMC to M.S.); institutional grant—Fundación Ramón Areces to the Centro de Biología Molecular ‘Severo Ochoa’; predoctoral fellowship from the Spanish Ministry of Education and Science (to V.C.L.L.). Funding for open access charge: BFU2008-00215/BMC. Conflict of interest statement. None declared.