Understanding the gender differences in agricultural productivity is crucial for formu-lating informed and effective policies to sustainably improve low productivity whichcharacterises agriculture in Sub-Sahara Africa. Using a panel dataset from the ICRISATled Tropical Legumes project III (2008–2013), we analyse the gender gap in theproduction of legumes in Malawi. Employing the Oaxaca–Blinder decompositionmethod allows decomposition of gender gap into the following: (i) the portion causedby observable differences in the factors of production (endowment effect) and (ii) theunexplained portion caused by differences in return to the same observed factors ofproduction (structural effect). We conducted the empirical analysis separately forpigeonpea and groundnut. Our findings reveal that for groundnut cultivated plots,women are 28% less productive than men after controlling for observed factors ofproduction; however, the gender gap estimated in the pigeonpea cultivated plots are notstatistically significant. The decomposition estimates reveal that the endowment effectis more relevant than the structural effect, suggesting that access to productive inputscontributes largest to the gender gap in groundnut productivity, and if women involvedhad access to equal level of inputs, the gap will be reduced significantly. The variationin the findings for groundnut and pigeon plot suggests that policy orientation towardsreducing gender productivity gap should be crop specific.