'Mal secco' is a serious disease of lemon and other citrus species, reduces lemon production, and limits the use of susceptible cultivars especially in the Mediterranean countries, against which there is no effective management system to control the disease. The objective of this study was to determine yield efficiency, tree and fruit characters, and molecular profiles of the selected promising genotypes in lemon breeding program to develop 'mal secco' tolerant lemon cultivars. After 4 years of evaluation, 'Tuzcu 894', a progeny of 'Finike Yerli Yuvarlak' and 'Kutdiken', was designated as promising genotype with high yield, fruit weight,juice content and low seed number contrary to 'Kutdiken' as control. Tuzcu 8911' was suitable for dense planting having the highest yield in CV. In addition, these two promising genotypes survived after many years being subjected to artificial and natural P. tracheiphila infections and harsh winter temperatures, which were attractive to the citrus industry. Molecular analysis, as assessed with 11 inter-simple sequence repeats (ISSR) primers. indicated that 'Tuzcu 09 Aklimon' and its selections, 'Tuzcu 896', 'Tuzcu 897' and 'Tuzcu 898', were distinct from the other genotypes with similarity value of 0.82. Genetic variation among the other lemon genotypes was low and some of the genotypes were identical. It was concluded that variations in the agronomical characters are mainly due to mutations. (C) 2009 Elsevier B.V. All rights reserved.