Divergent evolution between taxa adapted to contrasting environments is challenging at a microgeographic scale, where populations are within the dispersal neighbourhood of one another. This is because gene flow homogenises the allelic differences created by natural selection. However, strong selection against migrants and hybrids can mitigate the effects of gene flow. We report a case study of microgeographic adaptation in two ecotypes of the Australian wildflower Senecio lautus, which display heritable phenotypes adapted to sand dune and rocky headland environments. These sister taxa interbreed readily in the laboratory but show reproductive isolation in the field despite their parapatric distribution. By using phenotypic and genotyping-by-sequencing data in geographic cline analysis, we are able to quantify divergence in adaptive traits and allele frequencies, natural selection, and the strength of barriers to gene flow. We observe stepped clines in the allele frequency of nine diagnostic loci and in ten phenotypic traits at a spatial scale of less than 50m. The estimated strength of selection was absolute for several traits and barriers to gene flow were complete for some loci. Consistent with the accumulation of complete reproductive isolation between the two ecotypes, the centre of phenotypic and allelic clines were tightly concordant. Despite this, allele frequencies across the genome were homogenous and genetic differentiation was minimal with FST = 0.029, suggesting that divergence is recent. These findings are consistent with the prediction that extreme fitness differences conferred by as few as one locus can facilitate divergent evolution and potentially speciation irrespective of spatial scale.