ZOOTAXA ISSN 1175-5326 (Print Edition) & ISSN 1175-5334 (Online Edition)
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Most highly cited papers* (according to SCIE) 

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Checklist of catfishes, recent and fossil (Osteichthyes: Siluriformes), and catalogue of siluriform primary types  
CARL J. FERRARIS, JR.
(USA)
Zootaxa 1418: 1-628 (8 Mar. 2007Abstract & excerpt (PDF; 20KB) | Full article Part 1  & 2 (PDF; 4890KB) 
open access 
Times Cited in SCIE: 100 

A checklist of the current valid species of the subfamily Triatominae Jeannel, 1919 (Hemiptera, Reduviidae) and their geographical distribution, with nomenclatural and taxonomic notes
C. GALVÃO, R. CARCAVALLO, D. DA S. ROCHA & J. JURBERG (Brazil)
Zootaxa 202: 1-36 (2003) Abstract & excerpt (PDF; 10KB) | Full article (PDF; 200KB) Order PDF
Times Cited in SCIE:
98

New World direct-developing frogs (Anura: Terrarana): Molecular phylogeny, classification, biogeography, and conservation
S. BLAIR HEDGES, WILLIAM E. DUELLMAN, & MATTHEW P. HEINICKE (USA)
Zo
otaxa 1737: 1-182 (31 Mar. 2008
Abstract & excerpt (PDF; 20KB) | Full article (PDF; 6590KB)  Order PDF
Times cited in SCIE: 52

Foreword
J.K. LOWRY (Australia) & A.A. MYERS (Ireland)
Zo
otaxa
2260: 17-108 (8 Oct. 2009)
Abstract & excerpt (PDF; 20KB) | Full article (PDF; 2350KB) 
open access 
Times Cited in SCIE: 49

A revised catalog of the mite family Phytoseiidae
G.J. DE MORAES (Brazil) , J.A. MCMURTRY (USA), H.A. DENMARK (USA) & C.B. CAMPOS (Brazil)
Zootaxa
434: 1-494 (2004) Abstract & excerpt (PDF; 50KB) | Full article (PDF; 2600KB) Order PDF
Times cited in SCIE: 43

Tardigrade taxonomy: an updated check list of the taxa and a list of characters for their identification
R. GUIDETTI & R. BERTOLANI (Italy)
Zootaxa
845: 1-46 (1 Feb. 2005) Abstract & excerpt (PDF; 10KB) | Full article (PDF; 290KB) Order PDF
Times Cited in SCIE: 38

Venation pattern and revision of Orthoptera sensu nov. and sister groups. Phylogeny of Palaeozoic and Mesozoic Orthoptera sensu nov.
O. BÉTHOUX & A. NEL (France)
Zootaxa 96: 1-88 (2002) Abstract & excerpt (PDF; 10KB) | Full article (PDF; 1600KB)  Order PDF
Times Cited in SCIE: 3
8

Catalogue of the Cerambycidae (Coleoptera) of the Neotropical Region. Part II. Subfamily Lamiinae
M.A. MONNE (Brazil)
Zootaxa 1023: 1-760 (29 Jul. 2005
Abstract & excerpt (PDF; 10KB) | Full article A, B, C  (PDF; 5200KB) Order PDF
Times Cited in SCIE: 36

Zootaxa 1180: 1-172 (21 Apr. 2006) 69 plates; 250 references 
The morphology, higher-level phylogeny and classification of the Empidoidea (Diptera)
B.J. SINCLAIR (Germany) & J.M. CUMMING (Canada)
Abstract & excerpt (PDF; 10KB) | Full article part A, part B (PDF; 3900KB) 
open access 
Times Cited in SCIE: 34

A Catalogue of the Muscidae (Diptera) of the Neotropical Region
C.J.B. DE CARVALHO (Brazil), M.S. COURI (Brazil), A.C. PONT, D. PAMPLONA (Brazil) & S.M. LOPES (Brazil)
Zootaxa 860: 1-282 (2005Abstract & excerpt (PDF; 10KB) | Full article (PDF; 1740KB) Order PDF
Times Cited in SCIE: 32

* Listed here are only top 10 most-cited Zootaxa papers in SCIE (Science Citation Index Expanded)
See also most highly cited papers in Zootaxa according to Google Scholar

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Published  on 16 Jul. 2010