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The Marlborough Sounds has a coastline of 1500 km and hosts the greatest diversity of marine shag species in New Zealand. A survey of all breeding shag species was conducted in spring 2006. Apart from New Zealand king shag, 3 species were counted: spotted shag (Strictocarbo punctatus), pied shag (Phalacrocorax varius) and little shag (Phalacrocorax melanoleucos). Two other species (black shag Phalacrocorax carbo and little black shag Phalacrocorax sulcirostris) also occur in the area but were not recorded breeding. A total of 1,254 pairs of spotted shag were recorded at 193 sites, with most colonies occurring in the outer Sounds and inner Queen Charlotte Sound. Average colony size was 6.5 pairs (range 1-76 pairs), with 85% of colonies containing ≤10 pairs. The distribution of spotted shag colonies appears to be influenced by the availability of suitable cliff habitat. Breeding pied shags were found at 48 colonies, with a total of 438 pairs. Colonies were widely distributed, and average colony size was 9.1 pairs (range 1-28), with 83% containing ≤15 pairs. A total of 226 little shag pairs were found at 24 colonies, with most colonies also including nesting pied shags. Colony size was on average 9.4 pairs (range 4-24), with 75% of colonies containing ≤10 pairs. Colonies of pied shags and little shags were found mostly in native vegetation. Colonial seabirds that occur at relatively few locations can be used as indicators to establish critical thresholds for marine management and marine conservation. It is proposed that this survey provide a good baseline for such an approach in the Marlborough Sounds.