Previous attempts to map science using the co-citation clustering methodology are reviewed, and their shortcomings analyzed. Two enhancements of the methodology presented in Part I of the paper-fractional citation counting and variable level clustering—are briefly described and a third enhancement, the iterative clustering of clusters, is introduced. When combined, these three techniques improve our ability to generate comprehensive and representative mappings of science across the multidisciplinaryScience Citation Index (SCI) data base. Results of a four step analysis of the 1979SCI are presented, and the resulting map at the fourth iteration is described in detail. The map shows a tightly integrated network of approximate disciplinary regions, unique in that for the first time links between mathematics and biomedical science have brought about a closure of the previously linear arrangement of disciplines. Disciplinary balance between biomedical and physical science has improved, and the appearance of less cited subject areas, such as mathematics and applied science, makes this map the most comprehensive one yet produced by the co-citation methodology. Remaining problems and goals for future work are discussed.