Efficiency of morphological and physiological characteristics was studied for screening of sunflower (Helianthus annuus L.) inbred lines for drought tolerance in flowering stage using principle component analysis. Sixteen sunflower inbred lines were evaluated under rainout shelter for two years. According to the results stress tolerance index and stress susceptibility index each had more efficiency for identifying of drought tolerant and sensitive lines respectively. Principle component analysis was emerged as a powerful method for identifying of drought tolerant and sensitive lines which separated BGK 329 and RGK 21 as the most drought tolerant and sensitive lines respectively in the reverse direction of its biplot. The tolerant line was differentiated principally by higher plant height, stem and head diameter, seed weight, seed number, root and shoot dry weight, root length, leaf area, osmotic adjustment, Fv/Fm, SPAD value and seed yield and lower leaf temperature and specific leaf area compared to the sensitive line. Plant height, stem and head diameter were identified as morphological and leaf area, leaf temperature, Fv/Fm and SPAD value as efficient, none destructive physiological indicators for screening of sunflower genotypes under drought stress condition.