In this paper, we analyzed the microsatellites in the transcript sequences of the whole Laccaria bicolor genome. Our results revealed that, apart from the triplet repeats, length diversification and richness of the detected microsatellites positively correlated with their repeat motif lengths, which were distinct from the variation trends observed for the transcriptional microsatellites in the genome of higher plants. We also compared the microsatellites detected in the genic regions and in the nongenic regions of the L. bicolor genome. Subsequently, SSR primers were designed for the transcriptional microsatellites in the L. bicolor genome. These SSR primers provide desirable genetic resources to the ectomycorrhizae community, and this study provides deep insight into the characteristics of the micro satellite sequences in the L. bicolor genome.