The importance of root size system has long been recognized as crucial to cope with drought conditions. This investigation was conducted to: (i) evaluate the variability in root size system of hot pepper at maturity; (ii) estimate the effect of root size system on yield under drought conditions; and (iii) effect of water stress on xylem vessel development and total xylem cross-sectional area in roots of hot pepper cultivars. Twelve diverse hot pepper cultivars were grown in wooden boxes with two different water treatments, normal and in 50% water application as water deficit condition. Mean primary root length (PRL) showed a significant positive correlation with final fruit yield at normal as well as stressed condition. Total dry mass of fruit was reduced by 34.7% in drought treatments (DI) compared to full watered treatment (FI). At harvest, water-stressed plants had 21% lower root dry weight mass but higher root:shoot ratio other than FI. PRL, lateral root density, total xylem area per root cross-section showed a significant positive relationship with fruit yield. Also, lateral root density was higher in cultivars with higher xylem density, particularly in tolerant cultivars. Lateral root density ( r = 0.847, P < 0.001) and total xylem cross-sectional area in root ( r = 0.926, P < 0.001) were tightly related with total biomass production. The importance of root traits contributing to withstand drought in hot pepper is discussed.