The first step in the pathogenesis of bacterial pathogens is colonization of the host. During colonization, bacteria encounter host defenses, other commensal flora and selective pressures from lytic and temperate bacteriophage. Phages and bacteria have a long history of co-evolution, which has led to bacterial resistance mechanisms and phage counter-resistance mechanisms. One mechanism that phage have adapted is to provide a fitness advantage to the host during colonization and disease, thereby promoting survival of both bacteria and phages. Herein I examine how temperate phages affect streptococcal fitness while colonizing the host, specifically looking at the interactions between Streptococcus pneumoniae, phage element Spn1 and colonization of a murine nasopharynx. Temperate phages have been identified in the genomes of up to 70% of clinical isolates of Streptococcus pneumoniae. How these phages affect the bacterial host during colonization has not been previously demonstrated. To ask this question, we used a clinical isolate, which carries a novel prophage Spn1. Spn1 was detected as integrated and episomal forms both in vitro and in vivo. Surprisingly, Spn1 also expresses both lytic and lysogenic genes during normal growth conditions. Since Spn1 could not be spontaneously cured, a clean deletion was made to create the Spn1- strain. We used a competitive colonization assay in a murine model to test the fitness of the Spn1+ vs. the Spn1- strain. The Spn1- strain outcompeted the Spn1+ strain seventy-fold after seven days of colonization. To determine if Spn1 is causing a fitness defect by a trans-acting factor, we made an Spn1+ mutant that does not become an episome or express any phage genes. This mutant competed equally with the Spn1- strain, indicating that the fitness defect required expression of phage genes. Further experiments interrogating autolysis, chain length and resistance to lysis by penicillin indicated differences in the cell wall physiology associated with the presence of Spn1. This change in cell wall physiology may be responsible for the fitness defect of Spn1+ strain during colonization. This study provides new insight into how bacteria and prophages can interact and how these interactions may impact the relationship between bacteria and the host.