Extensive studies have been conducted to understand the genetic control of in vitro androgenesis, but little is know about the genes and the mechanisms involved in the switch that allows an immature pollen grain to develop as an embryo. We have developed two maize isogenic lines with high androgenetic aptitude, named AH5-44 and AH5-49, through backcross and selection from a high-responsive DH229 line on the non-responding A188 line genetic background. The genomic structure of these two lines was precisely described with microsatellite markers. Five regions retained from the parent DH229 highly responsive to androgenesis were localised in both AH5-44 and AH5-49. Sequences expressed on microspores extracted from the four lines were amplified using a cDNA-AFLP protocol. For each line, eight culture conditions were compared: microspores extracted after tassel recovery, after 7 or 14 days in cold room and after 1-4 days of in vitro culture. This genetic and developmental screening allowed us to identify four sequences, including a new HSP70-like candidate gene. Possible implication of the identified sequences in androgenesis response is discussed.