Banana finger drop is a dislodgement of individual fruits from the hand at the pedicel area. Recent findings led us to suggest developmental cues as additional factors, beside ethylene, acting to control the finger drop process. Assuming that this developmental control involved MADS-box components as shown in other fruit, we analyzed here the MADS-box gene expression in the median (control zone, CZ) and pedicel rupture (drop zone, DZ) areas of the peel tissue from banana harvested at different physiological stages. In immature fruits, the mRNA level of MaMADS1, MaMADS2 and MaMADS6 genes were transitorily enhanced in DZ as compared to control. In early mature green fruit, MaMADS2 and MaMADS5 mRNA were highly and transitorily induced in the DZ, with a peak observed at day 2, as compared to the CZ. MaMADS2, MaMADS3 and MaMADS4 mRNA accumulated at comparable levels in both zones. In late mature green fruit, all MaMADS genes were transiently and differentially induced according to the peel zone, except MaMADS6 that increased slightly without any marked change in CZ and DZ. The MaMADS3 mRNA level was comparable in both zones while that of MaMDAS4 was enhanced in DZ. In banana fruit, MaMADS box genes may participate in this sequence of events with MaMADS2 and MaMADS4, and to a lesser extent MaMADS5, being associated with finger drop. They act sequentially to control the process, with MaMADS2 and MaMADS5 beginning earlier and MaMADS4 acting later. Findings offer insights regarding upstream regulatory factors and roles of MADS genes associated with finger drop. For improving banana quality traits, comparative analysis of MADS box genes expression enables selecting candidate genes for molecular marker identification. Next steps may (i) identify related molecular marker(s) and (ii) validate these markers via genetic association studies on a segregating population.