Gene duplication and subsequent divergence can lead to the evolution of new functions and lineage specific traits. In sticklebacks, the successive duplication of the mucin-like gene (MUC19) into a tandemly-arrayed, multi-gene family has enabled the production of copious amounts of ‘spiggin’, a secreted adhesive protein essential for nest construction. Here we examine divergence between spiggin genes among three-spined sticklebacks (Gasterosteus aculeatus) from ancestral marine and derived freshwater populations, and propose underpinning gene duplication mechanisms. Sanger sequencing revealed substantial diversity among spiggin transcripts, including alternatively spliced variants and interchromosomal spiggin chimeric genes. Comparative analysis of the sequenced transcripts and all other spiggin genes in the public domain support the presence of three main spiggin lineages (spiggin A, spiggin B and spiggin C) with further subdivisions within spiggin B (B1, B2) and spiggin C (C1, C2). Spiggin A had diverged least from the ancestral MUC19, while the spiggin C duplicates had diversified most substantially. In silico translations of the spiggin gene open reading frames predicted that spiggin A and B are secreted as long mucin-like polymers, while spiggin C1 and C2 are secreted as short monomers, with putative anti-microbial properties. We propose that diversification of duplicated spiggin genes has facilitated local adaptation of spiggin to a range of aquatic habitats.