Genes differentially expressed between tetrasporophytes and female gametophytes of Gracilaria/Gracilariopsis lemaneiformis were isolated by suppression subtractive hybridization (SSH) and screened by dot-blot macro-arrays. Different expression profiles of selected clones based on the results of dot-blot macro-arrays were verified using virtual Northern blots. Totally, 14 phase relative cDNAs had been isolated and sequence identified. Among them, seven cDNAs were respectively homologous to crucial metabolic enzymes, Rab GTPase, RP42 homolog, and two hypothetical proteins, while the rest did not have significant hits in the databases examined. The results of virtual Northern blots revealed that 11 cDNAs were differentially expressed between the two samples, including 7 genes up-regulated in tetrasporophytes, 1 expressed exclusively in tetrasporophytes and 3 up-regulated in female gametophytes. By densitometric analysis relative to GAPDH, 8 cDNAs increased 1.3-4.2 fold and 3 decreased about 0.4-0.7 fold in tetrasporophytes compared to female gametophytes. The present study provides the first insight into genes that may involve in phase differentiation in G. lemaneiformis.