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The diversity of pulsed-field profiles (PFPs) within non-typhoidal <em>Salmonella</em> subtypes influences epidemiological analyses of <em>Salmonella</em> outbreaks. Therefore, determining the PFP diversity of each <em>Salmonella</em> serovar is important when evaluating current circulating strains. This study examined the PFP diversity of three important public health <em>Salmonella enterica</em> subspecies <em>enterica</em> serovars, <em>S.</em> Enteritidis (n=177), <em>S.</em> Infantis (n=205), and <em>S.</em> Corvallis (n=90), using pulsed-field gel electrophoresis. Isolates were collected from several sources, primarily from chicken-derived samples, in the Kyushu-Okinawa region of Japan between 1989 and 2005. <em>S.</em> Enteritidis isolates displayed 51 distinct PFPs (E-PFPs), with 92 (52.0%) and 32 (18.1%) isolates displaying types EPFP1 and E-PFP10, respectively. The 205 S. Infantis isolates showed 54 distinct PFPs (I-PFPs), with 87 (42.4%) and 36 (17.6%) isolates being I-PFP4 and I-PFP2, respectively. I-PFP18 was the dominant I-PFP of layer chicken isolates across a 5-year period. Fourteen distinct <em>S.</em> Corvallis PFPs were detected. Simpson’s index results for the genetic diversities of <em>S.</em> Enteritidis, <em>S.</em> Infantis, and <em>S.</em> Corvallis isolates were 0.70, 0.79, and 0.78, respectively. None of the EPFPs or I-PFPs of layer chicken isolates overlapped with those of broiler chicken isolates, and the dominant clonal lines existed for &gt;10 years. In conclusion, limited PFP diversities were detected amongst <em>S.</em> Enteritidis, <em>S.</em> Infantis, and <em>S.</em> Corvallis isolates of primarily chicken-derived origins in the Kyushu-Okinawa region of Japan. Therefore, it is important to take into account these limitations in PFP diversities in epidemiological analyses of <em>Salmonella</em> outbreaks.