Technical Abstract: The second International Symposium on Molecular Markers in Horticulture was held at the CH2M Hill Alumni Center at Oregon State University (OSU), Corvallis (Oregon, US), from July 29 to August 1st, 2009. This symposium was convened by a scientist at the National Clonal Germplasm Repository (NCGR) of the United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), with cooperation from OSU, and under the dual sponsorship of the ISHS Commissions of Biotechnology and Molecular Biology, and Plant Genetic Resources. Overall, 45 oral presentations and 40 posters were included in the program. Approximately 130 participants from 30 countries attended the symposium. Five sessions provided the focus for the symposium: 1) Molecular markers in identification and characterization; 2) Marker-assisted breeding (trait-specific markers); Applications of next-generation sequencing; 4) Analytical approaches and bioinformatics; and 5) Molecular markers in systematics, diversity and evolution. Each session was opened by a lecture from an invited keynote speaker and was moderated by an expert who organized each session.