Cross-breeding is the main method to create variation and cultivate new varieties.However, it is often due to unclear phylogenetic relationships between the parents that the hybrids many have similar genetic relationships and low genetic diversities.Inter family genetic diversity analysis was undertaken between eight Pinus elliottii × P.caribaea var.hondurensis families using ISSR markers.A total of 480 samples were analyzed by using 10 ISSR primers.Genetic diversity index of the families were between 0.0152~0.0872.And Shannon genetic diversity index were between 0.0216 and 0.1294 (intra-family index was 0.2934).Analysis showed that only a small proportion (25.65%) of genetic variation resided within families, while a large proportion (74.35%) inter-family genetic differentiation index of Gst=0.7435.According to the genetic distance and clustering analysis by UPGMA, the genetic differentiation among 8 families is relatively high, with low gene flow (Nm=0.1725).The gene flow of inter families may be related to the genetically high heterozygous of slash pine and caribbean pine.These findings are expected to provide some technical foundations for genetic breeding.