| Summary: | Leaf Twister Disease (LTD) is one of the major biotic constraints of onion cultivation in Sri Lanka. The present study was conducted to determine morphological and pathogenic variations among <em>Colletotrichum</em> and <em>Fusarium </em>isolates, causing LTD. Fungal isolates were obtained from LTD-infected onions, collected from 30 locations in the Jaffna district of Sri Lanka. The colony characters, spore dimension, colony growth rate and fungicide sensitivity in vitro and in vivo were used to determine the morphological variations of fungal isolates. Pathogenic variations of the fungal isolates in terms of pathogenicity and virulence were determined by in vivo inoculation assays using red onion (<em>Allium cepa L. </em>) variety Vethalan. Morphologically-different 29 isolates of <em>Colletotrichum</em> and 16 isolates of <em>Fusarium</em> were collected from different farmer fields of Jaffna district. Out of the 29 <em>Colletotrichum</em> isolates, six were identified as <em>C. gloeosporioides</em> by morphological features of fungal colonies and spores. Colony and spore morphology also resembled <em>C. acutatum</em> and <em>C. fragaria</em> among the <em>Colletotrichum</em> isolates associated with the LTD infections of onion. Colony growth rate and in vivo sensitivity to fungicide (Thiophanate-methyl 50% + Thiram 30% WP) were highly variable among the tested isolates of <em>Colletotrichum</em> and <em>Fusarium</em>. Recommended dosage of the fungicide completely inhibited the mycelia growth in vitro. However, the recommended dosage as only a single seed treatment did not completely control any isolate of <em>Colletotrichum</em> or <em>Fusarium</em> under in vivo conditions. Virulence of the <em>Colletotrichum</em> and <em>Fusarium</em> varied significantly among the isolates in terms of rapidity and extent of disease spread. The red onion variety Vethalan was not completely resistant against any isolate of the two fungal genera tested. The present study revealed that the morphological and pathogenic variations exist among different isolates of <em>Colletotrichum</em> and <em>Fusarium</em>causing LTD in red onion in Jaffna district of Sri Lanka.<p> </p><p>Tropical Agricultural Research Vol. 25 (3): 412-431 (2014)</p>
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