Sweet pepper (Capsicum annuum, L.) production during the hot-wet and hot-dry seasons in the lowland tropics is constrained by high temperature, flooding, and root diseases. AVRDC has developed a grafting technology for tomato production during the hot summer season and is now accepted by a growing number of farmers in Southeast Asia. Similar technology is being developed for sweet pepper to enhance yield and improve quality under flooding. Since 2002, several chili pepper lines from a wide collection including wild species were identified to have tolerance to flooding. In 2003, screening was expanded with the goal of identifying chili pepper lines for production in flood-prone areas or for use as rootstocks for sweet pepper production during the hot-wet season, when market prices are profitable. Selected lines from C. baccatum, C. frutescens and C. chacoense were most tolerant to flooding damage with survival rate greater than 45%. In 2004, 23 accessions were selected to evaluate outstanding lines as rootstocks for sweet pepper production during the hot-wet and hot-dry seasons. Significant correlations (P < 0.01) were detected among plant traits during both seasons. Most traits were negatively correlated with disease incidence indicating that resistance to disease may be enhanced by taller plant stature, larger rootstock stem diameter and higher root number. Significant differences in yield were observed among rootstocks in both seasons. Mean yield during the hot-dry season was 50% higher than the hot-wet season. This study has identified promising lines of chili rootstock for production of grafted sweet pepper during the hot-wet and hot-dry seasons in the lowland tropics.