MapSynteny is a macro in MS Excel® able to draw the relationship between genetic maps and large sequences (scaffolds, chromosomes, BACs, etc.). Based on tab-delimited blast results and some formulas a suitable image for synteny analysis or physical mapping can be obtained. Applications of this approach include: 1) Many important crop plants have few genomic resources. Those species are referred to as orphan crops. Often related species are rich sources of information. MapSynteny is a useful tool for take advantage of this information. 2) Another application is the macro-assembly of scaffolds to obtain relationships at the chromosome level. The scaffolds are large sequences produced by next generation sequencing assembling processes. This simple and versatile software can produce four types of outputs based on traditional linkage map figures (www.automatizacionysistemas.com/download.html).