Multi-parent crosses of recombinant inbred lines exist in many species for fine-scale analysis of genome structure and marker-trait association. These populations encompass a wide range of crossing designs with varying potential. AlphaMPSim is a flexible simulation program that is efficiently designed for comparison of alternative designs for traits with varying genetic architectures and biallelic markers with densities up to full sequence. A large pool of founder haplotypes can be supplied by the user, or generated via integration with external coalescent simulation programs such as MaCS. From these, diverse founders for multi-parent designs can be generated automatically, and users can compare designs generated from diverse pedigrees. Full tracking of identity by descent status of alleles within the pedigree is undertaken, and output files are compatible with commonly available analysis packages in R.