The objective of the present work was to see the relationship of molecular markers and incompatibility and try to elucidate the mechanism and inheritance of incompatibility. The clone Sea 6 is selfincompatible and ICS 1 selfcompatible and it is expected that F2 of this progenies segregate for selfcompatible plants. Self pollinations were evaluated in 68 F2 plants obtained by selfing TSH 516 (SCA 6 x ICS 1). The pollinations that reached 5% of setting were considered selfcompatible. The markers utilized were, 232 RAP), 77 AFLP and 33 microsatellites markers in the total of 342 markers. The X2 was utilized to test the 3:1 segregation. Regression analysis were utilized to see molecular markers that is correlated to self-incompatible characteristic. From 68 plant evaluations, 25 were selfcompatible and 43 selfincompatible. The X2 test indicated 3:1 segregation distortion at 5% level. For the regression analysis using 342 molecular markers, 19 were significative at 5%. Two of the most significative were sAU17960 and mTcCIR46 , respectively 40% and 17,6% of R2 This results showed that probably more than one locus is involved for incompatibility reaction in the case of ICS 1. It is interesting to test these 19 potential candidate in larger populations and also in other populations.