In order to identify fungi causing dieback and endophitic fungi, samples were collected from shoot tips of some trees in Sistan and parts of Kerman province. From shoot tips of trees, small pieces with the size of five mm cultivated in Patato Dextrose Agar (PDA) after surface disinfection by sodium hypochlorite. Microscopic slides prepared from fungi growing in culture medium in lactic acid 50%. Morphological characters of fungal structures were examined using light microscopy. A combination of morphological features including conidiomata (if present), conidiogenous loci, shape, size and septation of conidia and conidiophores have been used to identify the taxa. Extraction of genomic DNA performed based on CTAB method. Quality and quantity and of extracted DNA investigated through agarose gel electrophoresis and spectrophotometry. Then ITS region of the ribosomal DNA amplified using ITS1 and ITS4 primers and PCR products were sequenced. Sequences of taxa compared with other correlate and similar sequences in Gene Bank. With morphological data and nucleotide sequencing of ITS-rDNA region, two species of the genus Neoscytalidium including N. dimidiatum (on Ficus religiosa, Nerium oleander, Prunus armeniaca) and N. novaehollandiae (on Morus alba) were isolated from trees with dieback symptoms. Furthermore, four species of the genus Alternaria including A. alternata (Citrus reticulata, Juglans regia, Prunus dulcis), A. consortialis (on Nerium oleander, Prunus dulcis, Vitis vinifera), A. malorum (on Prunus armeniaca) and A. tenuissima (on Citrus sinensis) and two other taxa including Fusarium proliferatum (on Citrus paradisi, Elaeagnus angustifolia, Prunus persica) and Sarocladium strictum (on Salix aegyptiaca) are identified as endophitic fungi from shoot tips.