$Campylobacter\; jejuni$, the most common cause of bacterial diarrhoeal disease, is normally helical. However, it can also adopt straight rod, elongated helical and coccoid forms. Studying how helical morphology is generated, and how it switches between its different forms, is an important objective for understanding this pathogen. Here, we aimed to determine the genetic factors involved in generating the helical shape of $Campylobacter$. A C. $jejuni$ transposon (Tn) mutant library was screened for non-helical mutants with inconsistent results. Whole genome sequence variation and morphological trends within this Tn library, and in various C. $jejuni$ wild type strains, were compared and correlated to detect genomic elements associated with helical and rod morphologies. All rod-shaped C. $jejuni$ Tn mutants and all rod-shaped laboratory, clinical and environmental C. $jejuni$ and $Campylobacter\; coli$ contained genetic changes within the $pgp1$ or $pgp2$ genes, which encode peptidoglycan modifying enzymes. We therefore confirm the importance of Pgp1 and Pgp2 in the maintenance of helical shape and extended this to a wide range of C. $jejuni$ and C. $coli$ isolates. Genome sequence analysis revealed variation in the sequence and length of homopolymeric tracts found within these genes, providing a potential mechanism of phase variation of cell shape.