Phages and plasmids are mobile genetic elements that drive bacterial evolution through horizontal gene transfer. However, the distinction between these elements is blurred by the existence of prophage-plasmids or phage-plasmids, which can transfer horizontally as viruses and vertically within cellular lineages as plasmids. This study investigates gene flow between phage-plasmids, phages, and plasmids. The results show that phage-plasmids have a gene repertoire that overlaps with both phages and plasmids. By tracking recent recombination events, the study finds that phage-plasmids exchange genes more frequently with plasmids than with phages, and direct gene exchange between plasmids and phages is less common. Phage-plasmids can mediate gene flow between plasmids and phages, including the exchange of core functions, defense systems, and antibiotic resistance. Additionally, a combination of gene transfer and gene inactivation can result in the conversion of elements, such as the loss of genes turning PI-like phage-plasmids into integrative prophages or plasmids. Some of these converted elements have acquired conjugation-related functions, making them mobilizable by conjugation. The study concludes that phage-plasmids play a key role in gene transfer across mobile elements within hosts and can act as intermediates in the conversion of one type of element into another.Phages and plasmids are mobile genetic elements that drive bacterial evolution through horizontal gene transfer. However, the distinction between these elements is blurred by the existence of prophage-plasmids or phage-plasmids, which can transfer horizontally as viruses and vertically within cellular lineages as plasmids. This study investigates gene flow between phage-plasmids, phages, and plasmids. The results show that phage-plasmids have a gene repertoire that overlaps with both phages and plasmids. By tracking recent recombination events, the study finds that phage-plasmids exchange genes more frequently with plasmids than with phages, and direct gene exchange between plasmids and phages is less common. Phage-plasmids can mediate gene flow between plasmids and phages, including the exchange of core functions, defense systems, and antibiotic resistance. Additionally, a combination of gene transfer and gene inactivation can result in the conversion of elements, such as the loss of genes turning PI-like phage-plasmids into integrative prophages or plasmids. Some of these converted elements have acquired conjugation-related functions, making them mobilizable by conjugation. The study concludes that phage-plasmids play a key role in gene transfer across mobile elements within hosts and can act as intermediates in the conversion of one type of element into another.