The goal of the AMYLOMICS EU-project is to develop new robust enzymes for the starch and carbohydrate industries. For this purpose an efficient platform technology for enzyme screening, called Targeted Metagenomics, was developed. The processcomprises microbial enrichment techniques; massive parallel 454 FLX sequencing and sequence capture technology. In the project, anaerobic and microaerophilic enrichments of environmental samples from geothermal habitats in Iceland were prepared, using starch derivatives and other carbohydrate substrates. Thus, metagenomes of a moderate complexity, high diversity and enhanced evenness were generated, suitable for FLX sequencing and enriched in starch or other carbohydrate utilizing organisms. Few metagenomes of appropriate diversity and evenness, according to results of 16S rRNA sequence analysis, were selected for the high throughput sequencing. Due to the extent of the metagenome data, assembly of the sequence reads yielded high number of contigs and residual singletons with partial open reading frames (orfs). Reassembly of the metagenome sequence data with sequence capture reads covering regions flanking the original contigs/singletons resulted in merged and new contigs and increased number of complete orfs, including carbohydrate genes. In the lecture, the Targeted Metagenomics procedure and the outcome will be described as well as properties of few novel amylolitic enzymes retrieved through the procedure.