As for JCR 2013, JCR 2012, JCR 2011 and JCR 2010, I list the 40 most highly cited journals indexed by the ISI Web of Knowledge under the subject “ecology”. To give you a reference to the general journals: Nature is now (last year) at 41.456 (42.351), Science at 31.477 (33.611), Plos Biology at 9.343 (11.771), PNAS at 9.674 (9.809), and PLOS ONE at 3.234 (3.534).
| Rank ’14 (’13) | Journal | Publications | IF’14 | 5-yr IF ’14 |
| 1 (2) | TRENDS IN ECOLOGY & EVOLUTION | 70 | 15.35 | 19.82 |
| 2 (1) | ECOLOGY LETTERS | 163 | 13.04 | 16.78 |
| 3 (3) | Annual Review of Ecology Evolution and Systematics | 27 | 10.98 | 19.83 |
| 4 (4) | ISME Journal | 215 | 9.27 | 9.44 |
| 5 (6) | GLOBAL CHANGE BIOLOGY | 308 | 8.41 | 8.71 |
| 6 (5) | FRONTIERS IN ECOLOGY AND THE ENVIRONMENT | 62 | 8.22 | 9.88 |
| 7(9) | BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY | 10 | 7.24 | 5.1 |
| 8(8) | ECOLOGICAL MONOGRAPHS | 29 | 7.11 | 10.11 |
| 9 (15) | Methods in Ecology and Evolution | 144 | 6.64 | 7.39 |
| 10 (7) | GLOBAL ECOLOGY AND BIOGEOGRAPHY | 132 | 6.25 | 7.18 |
| 11 (11) | MOLECULAR ECOLOGY | 419 | 5.84 | 6.33 |
| 12 (12) | JOURNAL OF ECOLOGY | 151 | 5.69 | 6.31 |
| 13 (-) | WILDLIFE MONOGRAPHS | 6 | 5.63 | 5 |
| 14 (16) | PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES | 625 | 5.47 | 5.65 |
| 15 (19) | FUNCTIONAL ECOLOGY | 148 | 5.32 | 5.28 |
| 16 (25) | ECOGRAPHY | 130 | 5.29 | 5.57 |
| 17 (17) | ECOLOGY | 316 | 5 | 6.16 |
| 18 (22) | EVOLUTION | 287 | 4.97 | 5.25 |
| 19 (18) | JOURNAL OF BIOGEOGRAPHY | 192 | 4.86 | 5.12 |
| 20 (20) | JOURNAL OF APPLIED ECOLOGY | 175 | 4.75 | 5.93 |
| 21 (20) | JOURNAL OF ANIMAL ECOLOGY | 144 | 4.73 | 5.32 |
| 22 (24) | CONSERVATION BIOLOGY | 168 | 4.66 | 5.2 |
| 23 (26) | ECOLOGICAL APPLICATIONS | 159 | 4.45 | 5.51 |
| 24 (-) | Advances in Ecological Research | 12 | 4.32 | 4.82 |
| 25 (-) | Biogeosciences | 467 | 4.21 | 4.67 |
| 26 (32) | ECOSYSTEMS | 104 | 4.13 | 4.57 |
| 27 (23) | AMERICAN NATURALIST | 169 | 4.04 | 4.96 |
| 28 (28) | HEREDITY | 131 | 3.8 | 4.16 |
| 29 (27) | BIOLOGICAL CONSERVATION | 305 | 3.75 | 4.7 |
| 30 (-) | Molecular Ecology Resources | 127 | 3.57 | 4.99 |
| 31 (35) | JOURNAL OF VEGETATION SCIENCE | 134 | 3.56 | 3.75 |
| 32 (14) | DIVERSITY AND DISTRIBUTIONS | 120 | 3.53 | 5.36 |
| 33 (36) | PERSPECTIVES IN PLANT ECOLOGY EVOLUTION AND SYSTEMATICS | 32 | 3.48 | 4.33 |
| 34 (30) | LANDSCAPE ECOLOGY | 131 | 3.43 | 3.86 |
| 35 (31) | OIKOS | 160 | 3.37 | 3.93 |
| 36 (38) | AGRICULTURE ECOSYSTEMS & ENVIRONMENT | 329 | 3.32 | 3.99 |
| 37 (34) | Biology Letters | 190 | 3.25 | 3.67 |
| 38 (33) | JOURNAL OF EVOLUTIONARY BIOLOGY | 260 | 3.2 | 3.54 |
| 39 (39) | BEHAVIORAL ECOLOGY | 174 | 3.16 | 3.35 |
| 40 (37) | OECOLOGIA | 349 | 3.12 | 3.62 |
Note: this post was written April 9 2016 – I backdated it to Summer 2015 because this is the time when the JCRs came out.
theoretical ecology 
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It is not ISI anymore. ISI sold Science Citation Index to Thomson-Reuters. So, it is Thomson-Reuters Impact Factors. ISI was a non-profit organization, T-R is a for profit publisher.
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