To explore candidate genes responsible for the blue color of Selaginella uncinata (Desv. ex Poir.) Spring leaves, we used transcriptome sequencing to compare differential gene expressions in blue and red S. uncinata leaves selected based on morphological observations and pigment content. In total, we obtained 30 119 unigenes with an average length of 1133 bp, and we identified 1442 differentially expressed genes (DEGs). Among the 1442 DEGs, 886 were upregulated and 556 were downregulated in blue leaf samples. After verification of expression by quantitative real-time polymerase chain reaction (qRT-PCR) analysis, seven key enzymes and their encoding genes were identified as being involved in the chlorophyll and flavonoid metabolism pathways. These genes included Mg-chelatase (CHLH), light-dependent NADPH-Pchlide oxidoreductase (LPOR), chlorophyllase (Chlase; CLH), hydroxycinnamoyltransferase (HCT), chalcone synthase (CHS), MYB, and flavonoid 3'-hydroxylase (F3'H), which may be involved in the blue leaf coloration of S. uncinata. Results from this study implied that the primary pathway of pigment metabolism in S. uncinata may be the chlorophyll metabolism pathway rather than the anthocyanin biosynthesis pathway. It is possible that chlorophyll b (Chl b) may be transformed into chlorophyll a (Chl a) by an alternative pathway in which it is converted to Chlorophyllide b by CLH, and then transformed to Chl a without the involvement of CBR or HCAR.