The seeds from the plant Pentaclethra macrophylla, also known as Ugba, are widely consumed in South-Eastern Nigeria and play a huge socio-economic role in the lives of the people. The consumption of its fermented seeds has become a concern because fatalities after its consumption have been reported in many different local communities. The source of the food poisoning was not investigated or identified, and could be due to microbial proliferation before or after harvest. Post-harvest contamination by microorganisms may be due to poor handling during processing, storage, and sales. Recently, several strains of Proteus mirabilis were found in the seeds after molecular evolutionary analysis in our study. Seed samples from 10 geographical locations were sourced from trade and subjected to Illumina whole-genome sequencing. The strains were separated into different clades or monophyletic groups, which indicate distinct evolutionary lineages. P. mirabilis mode of existence in humans is known to be both intra- and extracellular, and in other bacteria like Listeria monocytogenes, certain lineages are more pathogenic than others. Here, our findings reveal that the factors driving the evolution of P. mirabilis strains in the seeds of Pentaclethra macrophylla analysed were driven by genetic drift or niche adaptations in addition to selective pressures like geographic location. The study shows the need for further research to identify mutation shifts and the resilient nature of the isolates. Tracking the genetic diversity of bacterial transmissions in Nigeria will help establish early warning systems for control of diseases that have public health significance.