A total of 502 Campylobacter jejuni isolates from poultry in 12 different European countries, where 10 of them are the largest poultry production countries in Europe, were examined by whole genome sequencing to examine the genomic diversity of fluoroquinolone resistant and susceptible C. jejuni across the poultry producing European countries and to determine whether the emergence of fluoroquinolone resistance among C. jejuni is related to the transmission through countries or the selection through fluoroquinolone use in the individual countries. A high genomic diversity was observed. The isolates clustered in four main clusters. All trees revealed that the isolates were clustered according to the presence/absence of the gyrA mutation causing fluoroquinolone resistance and ST-types. The cgMLST trees of only FQ-R and FQ-S isolates showed that isolates from the same country of origin were distributed into multiple clusters similarly to the trees combining FQ-R and FQ-S isolates. The different phylogenetic methods provided concordant results, but it is not known which is the most meaningful biologically for identify the country of origin. A strong association between specific clonal types and the emergence of fluoroquinolone resistance was observed, as was phylogenetics structuring, allele frequency and proliferation of specific lineages in the different countries. Allele frequency analysis showed association of geographical origin of poultry C. jejuni populations between Romania-Poland, Italy-Germany-England, Portugal-The Netherlands and USA-Luxemburg. Allele frequency and phylogenetic analysis indicated that the isolates from Finland were from a single population and different from C. jejuni populations from other European countries. Trade pattern and antimicrobial use in livestock were not significantly associated with allele frequency or populations of C. jejuni