The calcareous nannoplankton distribution has been determined from surface and subsurface water samples, and floating and moored sediment trap samples, taken during the Indonesian-Dutch Snellius-II Expedition in July 1984–May 1985 from the Banda Sea and adjacent seas, an area with seasonally changing upwelling and downwelling conditions. The surface water (0–5 m) coccolithophorid standing crop and species diversity were very low to zero, in the subsurface water (50–300 m) coccolithophorids were more abundant. A total of 36 living species were recorded. Seasonal changes in coccolithophorid abundance in the surface water and previous pigment data suggest that coccolithophorids are present but devoid of coccoliths during the northwest-monsoon in January–February. It seems that low salinity and nutrient depletion of the surface waters during the northwest-monsoon (January–February) restrict coccolith formation, since normal coccoliths do develop during the southeast-monsoon (August) when upwelling causes nutrient enrichment and normal salinity of the surface layer. During the change of the northwest- to the southeast-monsoon (May) conditions for calcification become more favourable. During the initial phase of this change the coccolithophorids produce malformed coccoliths. In the Flores and Java Seas further west the influence of the Banda Sea vertical mixing is limited and malformation persists in the surface and subsurface water during the southeast-monsoon. Two types of malformation as a result of incomplete calcification are found in placolith bearing species: (1) coccoliths with a weakly developed central tube that easily disintegrates and (2) placoliths with incomplete shields, but with a solid central tube.