Campylobacter jejuni is a frequently detected food-borne pathogenic bacterium. Clinical cases are mostly sporadic but campylobacteriosis can have serious consequences, such as the development of Guillain-Barré syndrome as well as diarrheal diseases. We examined 265 retail raw chickens from Korean markets for the presence of C. jejuni using the US Food and Drug Administration standard cultural method and multiplex polymerase chain reaction (mPCR). The mPCR-confirmed C. jejuni isolates were subtyped by pulsed field gel electrophoresis (PFGE) and flaA-typing for investigating the genetic diversity of the microorganism in retail raw chickens. Restriction enzymes SmaI and DdeI were used for PFGE and flaA-typing, respectively. Campylobacter spp. were found in 181 samples (68.3%) and C. jejuni in 100 samples (37.74%). For C. jejuni, 73 pulsotypes and 30 flaA types were detected. Antibiotic resistance tests performed by disk diffusion assay indicated that most C. jejuni isolates were resistant to tetracycline, nalidixic acid, and ciprofloxacin, and 87 composite types were revealed by PFGE, flaA-typing, and the antibiotic resistance tests. Our results show that the genetic diversity of C. jejuni isolates is very high and the correlation between genotype and antibiotic resistance was low even though many bacteria showed multi-drug resistance.