auxins are the key players in plant growth development involving leaf formation phototropism root fruit and embryo development auxin indole 3 acetic acid aux iaa are early auxin response genes noted as transcriptional repressors in plant auxin signaling however many studies focus on aux arf gene families and much less is known about the aux iaa gene family in brassica rapa b rapa here we performed a comprehensive genome wide analysis and identified 55 aux iaa genes in b rapa using four conserved motifs of aux iaa family pf02309 chromosomal mapping of the b rapa aux iaa briaa genes facilitated understanding cluster rearrangement of the crucifer building blocks in the genome phylogenetic analysis of briaa with arabidopsis thaliana oryza sativa and zea mays identified 51 sister pairs including 15 same species briaa briaa and 36 cross species briaa atiaa iaa genes among the 55 briaa genes expression of 43 and 45 genes were verified using genebank b rapa ests and in home developed microarray data from mature leaves of chiifu and rcbr lines despite their huge morphological difference tissue specific expression analysis of briaa genes between the parental lines chiifu and rcbr showed that the genes followed a similar pattern of expression during leaf development and a different pattern during bud flower and siliqua development stages the response of the briaa genes to abiotic and auxin stress at different time intervals revealed their involvement in stress response single nucleotide polymorphisms between iaa genes of reference genome chiifu and rcbr were focused and identified our study examines the scope of conservation and divergence of aux iaa genes and their structures in b rapa analyzing the expression and structural variation between two parental lines will significantly contribute to functional genomics of brassica crops and we belive our study would provide a foundation in understanding the aux iaa genes in b rapa.