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. 2007
Abstract & excerpt
(PDF; 20KB) | Full article Part 1  & 2 (PDF; 4890KB) 
open access 
Times Cited in SCIE: 2
61 

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: 163

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 (18 February 2004) 1282 references      
Abstract & excerpt
(PDF; 50KB) free | Full article (PDF; 2600KB) Order PDF
Times Cited in SCIE: 156 

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: 143

The morphology, higher-level phylogeny and classification of the Empidoidea (Diptera)
B.J. SINCLAIR (Germany) & J.M. CUMMING (Canada)
Zootaxa 1180: 1-172 (21 Apr. 2006) 69 plates; 250 references 
Abstract & excerpt (PDF; 10KB) | Full article part A, part B (PDF; 3900KB) 
open access 
Times Cited in SCIE: 83

Annotated checklist of the rotifers (Phylum Rotifera), with notes on nomenclature, taxonomy and distribution
HENDRIK SEGERS
(Belgium)
Zo
otaxa
1564: 1-104 (31 Aug. 2007
Abstract & excerpt (PDF; 20KB) free | Full article (PDF; 670KB)   open access 
Times cited in SCIE: 76

Zootaxa 1430: 1-86 (22 Mar. 2007) 26 plates; 168 references                           Accepted: 27 Feb. 2007
Systematics of the Palaearctic and Oriental lizard tribe Lacertini (Squamata: Lacertidae: Lacertinae), with descriptions of eight new genera
E. NICHOLAS ARNOLD (UK), OSCAR ARRIBAS (Spain) & SALVADOR CARRANZA (Spain)
Abstract & excerpt (PDF; 20KB) free | Full article (PDF; 1500KB) subscription required
Times cited in SCIE: 75

Lepidoptera phylogeny and systematics: the state of inventorying moth and butterfly diversity
Niels P.Kristensen (Denmark), Malcolm J. Scoble (UK) & Ole Karsholt (Denmark)
Zootaxa 1668: 699-747 (21 Dec. 2007) 9 plates; 163 references                       Accepted: 21 Nov. 2007
Abstract & excerpt (PDF; 20KB) free | Full article (PDF; 1110KB)   open access 
Times cited in SCIE: 75

Order Trichoptera Kirby 1813 (Insecta), Caddisflies
Ralph W. Holzenthal, Roger J. Blahnik, Aysha L. Prather & Karl M. Kjer (USA)
Zootaxa 1668: 639-698 (21 Dec. 2007) 1 plate;  89 references                          Accepted: 16 Nov. 2007
Abstract & excerpt (PDF; 20KB) free | Full article (PDF; 2470KB)   open access 
Times Cited in SCIE: 69

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:
64

* 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 10 Aug 2013