Campylobacter is the leading cause of bacterial foodborne infections worldwide and a major threat to food safety. The incidence of Campylobacter infection in Israel has increased from 31.0 to 101.8 per 100,000 population during the years 1999 to 2012 (3.3-fold), and among children < 1 year old - from 222.9 to 587.2 (2.3-fold). 80% of the infections were due to Campylobacter jejuni. Multi locus sequence type (MLST) – based analysis of ~ 500 C. jejuni isolates from human, animal and food sources in Israel found a high genetic diversity. The Israeli isolates belonged to 23 different clonal complexes (CC’s) and to 123 sequence types (STs). The most common Israeli CCs (21, 206, 353, 257) are also prevalent globally. Some common European CCs (45, 48) are rare in Israel, while ST 460 is relatively more frequent in Israel. Notably, Israel contributed 36 new STs to the Campylobacter PubMLST database, including four which were isolated only from poultry sources. However, the majority of isolates from animal and food sources shared common CCs and STs with the human isolates. Using the PubMLST database we were able to show that the Israeli human isolates could be genetically attributed to the meat sources most commonly consumed in Israel, poultry (70%) and cattle (30%). These results should guide public health authorities in planning control measures to reduce the high burden of Campylobacter illnesses in Israel.