Eucalyptus spp. are widely planted in Colombia as an important component of a growing paper and pulp industry. Leaf and shoot blight caused by Calonectria spp. was one of the first disease problems to emerge in these plantations. A survey of Eucalyptus plantations in four forestry regions of Colombia during 2016 resulted in a large number of Calonectria isolates from soil samples collected in the understories of trees having symptoms of Calonectria leaf and shoot blight. The aim of this study was to identify and resolve the phylogenetic relationships for these isolates using DNA sequence comparisons of six gene regions as well as morphological characters. From a collection of 107 isolates, seven Calonectria species residing in three species complexes were identified. Two of these represented undescribed species, namely C. exiguisporasp. nov. and C. guahibosp. nov.Calonectria parvispora and C. spathulata were the most commonly isolated species, each of which accounted for approximately 30% of the isolates. The results suggest that Colombia has a wide diversity of Calonectria spp. and that these could challenge Eucalyptus plantation forestry in the future.