Corn along with wheat and rice is one of the most important cereal crops in the world, hence its cultivation and production as a strategic crop being increased in the world and Iran. Iranian maize mosaic virus (IMMV) a member of Nucleorhabdovirus genus and Rhabdoviridae family was found in a corn field in Fars province in 1979. The virus host range is restricted to the family Gramineae and is one of the most destructive viruses of maize in Iran. IMMV-infected plants exhibit chlorotic stripes paralell to the main midrib in all or a part of the leaf. Although the almost complete nucleotide sequence of IMMV (Shiraz isolate) is available at GenBank, however there is no information on molecular variation of IMMV isolates in Iran. In this study, in order to detection and molecular comparison of IMMV isolates, in fall 2011 and spring and summer 2012, leaf corn and wheat samples with viral symptoms were collected in Isfahan, Chaharmahal-o-Bakhtiari, Lorestan and Fars provinces. Total RNA was extracted from leaf samples and used as template in RT-PCR with AMLF/AMLR primer pair amlifying a part of the polymerase gene of IMMV. Amplification of expected size of 720 bp segment confirmed infection of all corn samples and some wheat samples from Isfahan province (15 out of 70) to IMMV. This is the first report of wheat infection to IMMV in Isfahan province. For molecular comparisons, full length of IMMV nucleoccapsid protein gene (1480 bp) was amplified in RT-PCR using AMNupNHE/AMNloEcoRl primer pair in infected samples. Seven isolates representing different hosts and regions including Farrokhshahr (FZ2), Kouhdasht (ZK2), Daran (ZA9), Dastgerd (Bk1) and Shiraz (OZ1) isolates from maize and Joharestan (Gg2) and Ziar (GZ5) isolates from wheat were sequenced. Multiple allignment of nucleocapsid protein gene of our isolates and one isolate of IMMV (DQ186554) available at GenBank in nucleotide level revealed high identity ranging from 98.5% to 99.8% among isolates. Farrokhshahr isolate (FZ2) showed the lowest identity with other isolates. This isolate showed the lowest (98.5%) and highest identity (98.9%) with Bk1 isolate and ZK2 and ZA9 isolates, respectively. The ZK2 isolate showed the highest identity (99.8%) with OZ1 isolate and the lowest identity (98.9%) with FZ2 isolate. In phylogenetic analysis, the isolates were divided into two subgroups, however no correlation was found between hosts and geographical regions.