evolution and genetic architecture of chromatin accessibility and function in yeast chromatin accessibility is an important functional genomics phenotype that influences transcription factor binding and gene expression genomescale technologies allow chromatin accessibility to be mapped with highresolution facilitating detailed analyses into the genetic architecture and evolution of chromatin structure within and between species we performed formaldehydeassisted isolation of regulatory elements sequencing faireseq to map chromatin accessibility in two parental haploid yeast species saccharomyces cerevisiae and saccharomyces paradoxus and their diploid hybrid we show that although broadscale characteristics of the chromatin landscape are well conserved between these species accessibility is significantly different for 947 regions upstream of genes that are enriched for go terms such as intracellular transport and protein localization exhibit we also develop new statistical methods to investigate the genetic architecture of variation in chromatin accessibility between species and find that cis effects are more common and of greater magnitude than trans effects interestingly we find that cis and trans effects at individual genes are often negatively correlated suggesting widespread compensatory evolution to stabilize levels of chromatin accessibility finally we demonstrate that the relationship between chromatin accessibility and gene expression levels is complex and a significant proportion of differences in chromatin accessibility might be functionally benign