Pork and pork products have been identified as a significant source of Salmonella infection, which is a major public health concern. The contamination of Salmonella on pork can happen both on farms (before slaughter) and at abattoirs (after slaughter). Salmonella isolates were collected from both feces on farms and lymph nodes in the abattoir to determine if contamination at abattoirs can be linked back to the farms of origin. Molecular subtyping of the isolated Salmonella was performed using amplified fragment length polymorphism (AFLP), a Polymerase chain reaction-based, high-throughput, relatively inexpensive method. In this paper, we develop a permutation test for the genetic association of Salmonella isolated on-farm and at-abattoir using the AFLP data. Simulation studies show that the proposed permutation test controls the type I error rate appropriately as well as possesses high power. An application of the proposed permutation test to the real Salmonella ALFP data results in a p-value of 0.038 which shows strong evidence of association between Salmonella isolated on-farm and at-abattoir.