This paper reports the identification and analysis of the primary structure of three novel metallothionein cDNA sequences in the gudgeon, Gobio gobio (Cyprinidae). Two different 180 bp coding regions were identified, resulting in two MT isoforms differing in one amino acid. The primary structure of the amino acid sequence was compared to other cyprinid MT sequences. Furthermore, two differently sized cDNAs were discovered in one of the two transcripts. We present a phylogenetic comparison of our sequences to other, previously published cyprinid MT gene sequences. Our analysis reveals an unexpected complexity in cyprinid MT evolution, with at least three gene duplication events. Differences and homologies between the evolution of cyprinid MT genes are compared to other teleost families. Finally, possible implications for metallothionein classification are discussed.