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<i>Vibrio parahaemolyticus</i> is one of the significant seafood-borne pathogens causing gastroenteritis in humans. Clustered regularly interspaced short palindromic repeats (CRISPR) are commonly detected in the genomes of <i>V. parahaemolyticus</i> and the polymorphism of CRISPR patterns has been applied as a genetic marker for tracking its evolution. In this work, a total of 15 pandemic and 36 non-pandemic <i>V. parahaemolyticus</i> isolates obtained from seafood between 2000 and 2012 were characterized based on hemolytic activity, antimicrobial susceptibility, and CRISPR elements. The results showed that 15/17 of the <i>V. parahaemolyticus</i> seafood isolates carrying the thermostable direct hemolysin gene (<i>tdh</i>+) were Kanagawa phenomenon (KP) positive. The Multiple Antibiotic Resistance (MAR) index ranged between 0.1 and 0.4, and 45% of the isolates have an MAR index ≥ 0.2. A total of 19 isolates were positive for CRISPR detection, including all <i>tdh</i>+ <i>trh</i>− isolates, two of <i>tdh</i>− <i>trh</i>+, and each of <i>tdh</i>+ <i>trh</i>+ and <i>tdh</i>− <i>trh</i>−. Four spacer types (Sp1 to Sp4) were identified, and CRISPR-positive isolates had at least one type of spacer homolog to the region of <i>Vibrio alginolyticus</i> megaplasmid. It is of interest that a specific CRISPR profile and spacer sequence type was observed with correlations to the hemolysin genotype (<i>tdh/trh</i>). Thus, these provide essential data on the exposure of foreign genetic elements and indicate shared ancestry within different genotypes of <i>V. parahaemolyticus</i> isolates.