The Rsv4 gene confers resistance to all the known strain groups of SMV in soybean [Glycine max (L.) Merr.]. The objective of this study was to construct a fine genetic map near Rsv4. Sequences of Rsv4-linked markers derived from expressed sequence tags (ESTs) showed high similarity with gene sequences of a transformation-competent artificial chromosome (TAC) clone of the model legume Lotus japonicus. This information was integrated with a comparative genomics approach, utilizing Lotus genome sequence information. A marker developed from one of soybean homologous ESTs of Lotus genes within a TAC was mapped to the other side of the Rsv4 gene. The results suggested that the Rsv4 soybean chromosomal region is microsyntenic with the Lotus chromosomal region. The identification of the microsyntenic region facilitated the development of additional 3 markers. Several other markers developed in this study were mapped to putative homoeologous or duplicated chromosomal regions in soybean. This targeted comparative mapping serves to provide a foundation for marker-assisted selection and cloning of the Rsv4 gene.