Mature fruit abscission (MFA) is a genetically controlled process, through poorly characterized mechanisms in fleshy fruit that include extensive transcriptional changes. While global transcriptome analyses have been used to investigate immature fruit abscission in fleshy fruit, no global gene expression changes specific to MFA have been described. Here we use pyrosequencing to characterize the transcriptomes of the olive abscission zone (AZ) during cell separation in order to understand MFA control at the stage of AZ activation. Analysis of gene expression from these AZs reveals that membrane microdomains involving sterols/sphingolipids and remorins together with signaling proteins are potentially involved in MFA. This is accompanied by gene activity related to sphingolipid turnover, suggesting potentially the involvement of long-chain base metabolism in regulating MFA. Activation of vesicle trafficking involving small GTPases is probably required for cell wall modifications during abscission. Analysis of transcription factors indicates that most members of the MYB and bZIP families are abundantly represented in the fruit AZ, and is consistent with a model by which most of the key transcription factors during abscission may regulate downstream processes mostly related to ABA. The data provide the first thorough analysis available for a comprehensive picture of the array of cellular responses controlled by gene expression that lead to MFA in fleshy fruit.