Foodborne illness associated with O157:H7 ( O157) and romaine lettuce is a serious and persistent food safety issue. This study investigated the ability and associated genetic traits of five O157 strains-namely 86-24, 93-111, C7927, MF1847, and 505B-to internalize in romaine lettuce grown in soil and hydroponic systems. The results showed significant variations in the strains' ability to internalize, with soil cultivation being more susceptible to O157 internalization relative to hydroponics. Whole-genome comparisons and an analysis of the five O157 strains revealed insights into the potential genetic traits associated with internalization capacity. A single unique gene, ORF-4296, was found to be present in all four internalizing strains (86-24, 93-111, C7927, and MF1847), but absent in the non-internalizing strain 505B. Immediately downstream of OFR-4296 is the PhoQ/PhoP operon, which regulates the important stress responses of O157. Our data showed that this operon was identical in the four internalizing strains but different in strain 505B. Specifically, the C-terminal of PhoQ in strain 505B had a distinct amino acid sequence. The inability of 505B to internalize may be linked to its lack of ORF-4296 and its distinctive C-terminal sequence of PhoQ.