Wild arable plants can be an economic burden but they also support diverse arable food webs and contribute to valuable ecosystem functions. These benefits may have been compromised over recent decades by declining weed diversity. The decline in wild arable plant diversity has been viewed predominantly in terms of species shifts a view that ignores the genetic and functional variation existing within species and the impact on ecological and evolutionary processes which this may have. To examine within-species diversity, ISSR markers were used in parallel with environmental and phenotypic characterisation, to investigate the population structure and diversity of Capsella bursa-pastoris (shepherd's purse) from arable fields in the UK. Analysis of 338 ISSR products for 109 individuals from 51 accessions obtained from the seed banks of 33 arable fields showed that in-field populations of shepherd's purse were genetically differentiated between individuals, and among accessions and fields. In addition, cluster analysis identified three genetically distinct regional-scale populations. Phenotypic variation was present at all scales of genetic differentiation, including the regional scale where populations differed in their key life-history traits: flowering time, fecundity and dormancy. Genetic drift is proposed as a contributor to differentiation among genetically isolated but locally co-occurring accessions. In addition, the genetic and phenotypic variation in shepherd's purse exhibited large scale, spatial trends and showed statistically significant associations with cropping intensity and soil-pH. These results suggest that adaptation as a result of selection by cropping practise and soil-pH has played a role in the ability of shepherd's purse to colonise and persist in arable fields.