Here, we take advantage of next generation sequencing (RNAseq) data that was generated for H. annuus, H. debilis and H. petiolaris populations. Our objectives were to (i) confirm the genetic relationship among samples, then (ii) determine the effect of selection on protein coding evolution and finally (iii) investigate the effect of genomic factors which, based on previous studies, are expected to co-vary with rates of protein coding divergence. In turn, this will reveal if patterns observed in previous studies comparing more distantly related taxa also hold on shorter evolutionary timescales in recently diverged wild sunflowers.