Abstract Using 15 simple sequence repeat (SSR) mi- crosatellite DNA loci, we analyzed genetic variation within Cocos nucifera germplasm collections at two locations in south Florida, representing eight cultivars. The loci were also used in a parentage analysis of proge- ny of the ‘Fiji Dwarf’ variety at both locations. A total of 67 alleles were detected, with eight the highest num- ber at any one locus. These loci identified 83 of the 110 individual palms. Gene diversity of the 15 loci ranged from 0.778 to 0.223, with a mean of 0.574. ‘Fiji Dwarf’, ‘Malayan Dwarf’, ‘Green Niño’ and ‘Red Spicata’ culti- vars resolve as distinct clusters in a neighbor joining tree using modified Rogers distance, while the tall varieties form two aggregates. The highest gene diversity was found in the tall cultivars (H ˆ = 0.583 cumulatively), and the lowest in the ‘Malayan Dwarf’ (H ˆ = 0.202). After the tall coconuts, the ‘Fiji Dwarf’ was most genetically diverse (H ˆ = 0.436), and had the largest number of unique alleles. Genetic identity is highest among the ‘Malayan Dwarf’ phenotypes, and between the tall vari- eties. The ‘Red Malayan Dwarf’ is genetically distinct from the ‘Green’ and ‘Yellow Malayan Dwarf’ pheno- types, which cannot be distinguished with the SSR loci used. Off-type ‘Malayan Dwarf’ phenotypes (putative hybrids with talls) can be identified genotypically. Par- entage analyses of 30 ‘Fiji Dwarf’ progeny propagated from five adults surrounded by other cultivars estimate that only 20% of the progeny were out-crossed to the other varieties, while 40–46% were possible selfs. This suggests that a seed-production orchard of the variety maintained at reasonable distance from other varieties, will likely yield only ‘Fiji Dwarf’ genotypes. Our data are discussed in the context of hypotheses of coconut dissemination around the world. Keywords Arecaceae · Palmae · SSR · Breeding · Parentage analysis · Tropical horticulture · Palm Introduction Cocos nucifera L., the coconut, is grown throughout the tropics as a plantation crop yielding several agronomic products that are important to export economies in these regions (Beck and Balick 1990; Harries 1995). In the United States, the coconut is, with minor exception, exclusively a tropical ornamental, much in demand as a signature tropical landscape element (Meerow 1992). In the 1970s, the Lethal Yellowing (LY) phytoplasma devastated the coconut canopy of south Florida. By 1983, the epidemic had destroyed an estimated 100,000 coconut palms (Howard and Barrant 1989). The loss of this palm tree canopy was considered detrimental enough to Florida’s tourism economy that the Florida State Legislature funded a research program during the epidemic with two main components. Similar efforts were also established by the Jamaican Coconut Industry Board (Harries 1973). Research centered at the Universi- ty of Florida Fort Lauderdale Research and Education Center (UF) concentrated on the disease organism and its vector, as well as seeking potential management or cura- tive strategies (McCoy et al. 1983). Subsequently, a coconut breeding program to develop new resistant vari- eties and seed orchards of known resistant cultivars was established at the USDA Subtropical Horticulture Re- search Station (“Chapman Field”) by the Florida Depart- ment of Agriculture and Consumer Services (FLDACS) Division of Forestry. As a result, significant coconut germplasm collections were developed at both locations, though direct funding for both programs was terminated in the 1980s (UF) and 1996 (FLDACS), respectively. Communicated by C. Möllers A.W. Meerow ( ✉ ) · R.J. Wisser · J.S. Brown · D.N. Kuhn R.J. Schnell USDA-ARS-SHRS, National Germplasm Repository, 13601 Old Cutler Road., Miami, FL 33158, USA e-mail: miaam@ars-grin.gov Tel.: 305-254-3635, Fax: 305-969-6410 T.K. Broschat University of Florida, Fort Lauderdale Research and Education Center, 3205 College Avenue, Fort Lauderdale, FL 33314, USA Theor Appl Genet (2003) 106:715–726 DOI 10.1007/s00122-002-1121-z Alan W. Meerow · Randall J. Wisser J. Steven Brown · David N. Kuhn Raymond J. Schnell · Timothy K. Broschat Analysis of genetic diversity and population structure within Florida coconut (Cocos nucifera L.) germplasm using microsatellite DNA, with special emphasis on the Fiji Dwarf cultivar Received: 25 March 2002 / Accepted: 28 June 2002 / Published online: 24 October 2002 © Springer-Verlag 2002