A method of selective polynucleotide sequencing, comprising: a) providing a plurality of amplification oligonucleotides immobilized on a solid support; b) hybridizing a population of oligonucleotide probes to a subset of the amplification oligonucleotides to produce a population of hybridized amplification oligonucleotides, each of the oligonucleotide probes comprising a first portion complementary to one or more of the amplification oligonucleotides and a second portion comprising a sequence from a selected region of a template polynucleotide; c) performing an extension reaction to extend the hybridised amplification oligonucleotides to produce a population of capture oligonucleotides immobilized on the solid support, each of the capture oligonucleotides comprising a sequence complementary to a selected region of a template polynucleotide; wherein the capture oligonucleotides comprise at least 10 different capture sequences; d) selectively hybridizing a population of template polynucleotides to the capture oligonucleotides to produce a population of hybridized capture oligonucleotides, wherein each of the template polynucleotides comprises a 5' adapter sequence identical to at least a portion of the amplification polynucleotides that remain unextended; e) extending the hybridized capture oligonucleotides to generate a population of extension products, each of the extension products having a first portion complementary to a template polynucleotide and a second portion complementary to at least a portion of the unextended amplification oligonucleotides; f) amplifying the extension products by annealing one or more of the unextended amplification oligonucleotides to one or more of the extension products, thereby producing a plurality of solid-phase amplification products; and g) sequencing the solid-phase amplification products to obtain at least partial nucleotide sequences of the template polynucleotides. a) providing a plurality of amplification oligonucleotides immobilized on a solid support; b) hybridizing a population of oligonucleotide probes to a subset of the amplification oligonucleotides to produce a population of hybridized amplification oligonucleotides, each of the oligonucleotide probes comprising a first portion complementary to one or more of the amplification oligonucleotides and a second portion comprising a sequence from a selected region of a template polynucleotide; c) performing an extension reaction to extend the hybridised amplification oligonucleotides to produce a population of capture oligonucleotides immobilized on the solid support, each of the capture oligonucleotides comprising a sequence complementary to a selected region of a template polynucleotide; wherein the capture oligonucleotides comprise at least 10 different capture sequences; d) selectively hybridizing a population of template polynucleotides to the capture oligonucleotides to produce a population of hybridized capture oligonucleotides, wherein each of the template polynucleotides comprises a 5' adapter sequence identical to at least a portion of the amplification polynucleotides that remain unextended; e) extending the hybridized capture oligonucleotides to generate a population of extension products, each of the extension products having a first portion complementary to a template polynucleotide and a second portion complementary to at least a portion of the unextended amplification oligonucleotides; f) amplifying the extension products by annealing one or more of the unextended amplification oligonucleotides to one or more of the extension products, thereby producing a plurality of solid-phase amplification products; and g) sequencing the solid-phase amplification products to obtain at least partial nucleotide sequences of the template polynucleotides.