Elm (Ulmus, Ulmaceae) is one of the most popular and important trees in urban and landscape areas in Iran. A severe decline of elm trees has recently been observed in some areas of Kerman and Shiraz cities. However, the identity of the causal agents has not yet been investigated. The purpose of this study, carried out in the years 2012–2014, was to isolate and identify fungal trunk pathogens associated with decline symptoms observed in elm trees. Samples were collected from trunks and branches of trees showing various disease symptoms and internal wood lesions. Fungal isolations were made from discolored or decayed wood tissue. In Kerman some elm trees were attacked by the beetle Aeolesthes sarta; therefore, samples were also collected from larvae and adults of beetles associated with trees showing wood damage. Fungal isolates were identified by morphological, cultural and molecular characteristics. Thirteen fungal species, Phaeoacremonium (P.) minimum, P. parasiticum, P. sicilianum, P. alvesii, P. fraxinopennsylvanicum, Spencermartinsia viticola, Dothiorella (Do.) sarmentorum, Neoscytalidium hyalinum, Diatrype (Di.) whitmanensis, Cosmospora viridescens, Phoma (Pho.) herbarum, Phellinus (Phe.) tuberculosus and Inonotus levis were identified. Phaeoacremonium parasiticum was the only species isolated from both larvae and adult beetles. Pathogenicity trials were performed on detached shoots of elm under greenhouse conditions. Dothiorella sarmentorum was the most virulent species based on the length of wood necrosis. This study is the first report of P. sicilianum, C. viridescens and Phe. tuberculosus in Iran. In addition, most of the isolated species are reported for the first time on elm trees in the world.