Data package includes data and R code for the examination of geospatial genetic structure (SGS) and simulation of inbreeding in giant kelp (Macrocystis pyrifera) from the Santa Barbara Channel, California. Data are reported for microsatellite markers from individual giant kelp plants from Carpinteria Reef, Mohawk Reef and Goleta Bay, collected during September 2009. Relative X and Y coordinates (meters) were recorded for each specimen sampled. R code consists of two scripts, a) to calculate mean number of alleles per locus, and observed and expected heterozygosity, and b) to simulate self-fertilization and sibling/cousin relationships. These data were presented in: Johansson, Mattias L, Raimondi, Peter T, Reed, Daniel C, Coelho, Nelson C, Serrão, Ester A, Alberto, Filipe A. In press. Looking into the black box: simulating the role of self-fertilization and mortality in the genetic structure of Macrocystis pyrifera. Molecular Ecology, 22:4842–4854. These data are also available from: Johansson ML, Raimondi PT, Reed DC, Coelho NC, Serrão EA, Alberto FA (2013) Data from: Looking into the black box: simulating the role of self-fertilization and mortality in the genetic structure of Macrocystis pyrifera. Dryad Digital Repository. doi:10.5061/dryad.s1b07.