Islet1/Isl1 is a LIM homeobox transcription factor with multiple functions during specification, maturation, proliferation and survival of various pancreatic cell types. While the conserved expression in the developing and mature vertebrate pancreas suggests a conserved function, neither the molecular basis for the diverse pancreatic requirements nor the developmental functions in a model other than the mouse had been addressed so far. Here, a combination of genetic, molecular and in vivo imaging approaches in the model organism zebrafish is used in order to address the function of Isl1 in vertebrates. In isl1 mutant fish, endocrine cells are specified in normal numbers but more than half of these cells fail to establish expression of endocrine hormones. By using a lineage tracking approach, I show that Isl1 functions are different depending on the cell type. In addition, I find that isl1 expression in the pancreatic mesenchyme overlaps with that of the related genes islet2a/isl2a and islet2b/isl2b. While isl1 mutants already display a reduction of exocrine tissue, a combined block of two or three isl1/2 genes results in a stronger, dose-dependent reduction of exocrine tissue. To address the late cell type specific transcriptional functions, I created a strategy for inducible, lineage specific knockout of isl1 in zebrafish. As the regulatory elements driving isl1 expression in the endocrine pancreas have not yet been found, I used a bacterial artificial chromosome (BAC) containing the isl1 gene and potentially the regulatory sequences for expression of a targeting construct in the hormone producing cells. This system would allow the fluorescent labeling and tracking of Isl1 expressing cells. In addition, adding a short peptide to the Isl1 protein can be used for subsequent biochemical analysis. Lastly, LoxP-sites flanking the second exon of the isl1 gene will serve for cell type specific ablation of Isl1. To gain a better understanding about the molecular functions of Isl1, I analyzed the expression of potential Co-Activators. RT-qPCR based screening in embryonic and adult pancreatic samples revealed a list of 12 candidate genes. RNA in-situ hybridization uncovered expression of 5 genes in the adult zebrafish endocrine pancreas, while the expression of 1 gene was restricted to the exocrine compartment. Subsequent biochemical analysis by Co-Immunoprecipitation (Co-IP) showed that at least two of the proteins (Ldb1a and Ldb2a) are able to bind in vitro to Isl1.