Coastal Louisiana looses three million acres of wetlands annually due to natural and human interventions, which is ~80% of the coastal wetland loss nationally. Smooth cordgrass (Spartina alterniflora Loisel) is a warm season grass, which is utilized extensively as an ecosystem engineer to stabilize and reclaim coastal marshes along the Atlantic and Gulf coasts of North America because of its aggressive spreading ability and tolerance to salinity. However, Vermilion (CP8) is the only released cultivar extensively grown in coastal restoration projects, which could have serious repercussion in terms of genetic vulnerability to biotic and abiotic stress outbreaks. Therefore, recent breeding effort at the LSU Agricultural Center’s Coastal Plants Program is directed toward developing superior yet genetically diverse smooth cordgrass accessions for wetlands restoration and reclamation. The present research was conducted to assess the genetic diversity among 13 elite clones of smooth cordgrass (CP1 through CP13) including six soon-to-be-released clones using 23 genomic and expressed sequence tag-derived simple sequence repeat markers (g/eSSRs), and 32 randomly amplified polymorphic DNA (RAPD) markers. Altogether 276 polymorphic markers were generated where RAPD and SSR markers generated an average polymorphism percentage of 57.3% and 56.7%, respectively. Both marker systems showed a comparable value of expected genetic diversity per locus (SSR - 0.33; RAPD - 0.35). At 0.20 similarity coefficient four major clusters were observed: Cluster I (CP1, CP2, CP3, and CP6), Cluster II (CP5, CP8, and CP10), Cluster III (CP4, CP12, and CP7), and Cluster IV (CP9, CP11, CP13). Principal coordinate analysis (PCoA) supported the cluster analysis where the genotypes explained for 30% of the variation. Analysis of molecular variance (AMOVA) showed 62% genetic variation within a group as compared to 38% among groups (Fst = 0.38), which suggested the presence of enough genetic diversity among the accessions for exploitation in breeding program for further improvement.