Surveys of mitochondrial DNA (mtDNA) variation in the giant tiger prawn, Penaeus monodon, using restriction fragment length polymorphisms have provided the first clear evidence that the Indo-West Pacific region is a site of accumulation of genetic diversity rather than a site of origin of genetic diversity. No haplotyes were found in common between a group of five southeast African populations and a group of five Australian (including Western Australia) and three southeast Asian populations. The dominant haplotype was different in the Australian and southeast Asian population groups. Genetic diversity (pi) was greatest in Indonesia (pi averaged 0.05), less in the Philippines and Australia (pi averaged 0.01), and markedly less in the southeast African and the West Australian populations (pi averaged 0.003). The high diversity of the southeast Asian populations resulted from the occurrence in those populations of a set of haplotypes found only in southeast Asia but derived from the southeast African haplotypes. These genetic variants therefore evolved in the Indian Ocean and later migrated into the Indo-West Pacific region. Low genetic variation in the geographically marginal populations in southeast Africa and Western Australia is considered to be the result of bottlenecks, but mismatch distributions suggest that large population sizes have been maintained in Indonesian populations for long periods.

Indonesia has a long history of aquaculture, dating from the 15th century. Subsequently, the country has become a significant contributor to global aquaculture production, destined for both international and domestic markets. In 2009 the Government of Indonesia announced its vision to see Indonesia become the highest (volume) producer of aquaculture products in the world by 2015, with production targets equivalent to an overall increase in production of 353% between 2009 and 2014. This paper comprises a PEEST (policy, economic, environmental, social, technical) review undertaken as a background study for a SWOT (strengths, weaknesses, opportunities, threats) analysis, the outcomes of the SWOT analysis and a discussion of possible approaches to support sustainable aquaculture development in Indonesia. To meet the vision of a dramatic expansion of aquaculture production, one or more of the following strategies is required: intensification and production segmentation, areal expansion, and/or production diversification. Most likely the continued development of aquaculture in Indonesia will be a combination of these three strategies, with the relative influence of each depending on production sector and market demands. A key issue identified in the PEEST review and SWOT analysis is the dominance (in terms of number) of Indonesian aquaculture by smallholder aquaculture farmers. We argue that a range of influences, including aquaculture production expansion and changing international market requirements, have the potential to negatively impact smallholder aquaculture farmers in Indonesia, and that further policy development should specifically address these issues.

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