Circadian clock has been found in all forms of life from bacteria to humans. Its biological function is thought to provide organisms with time keeping ability, which enables organisms to control their behavioral, physiological and cellular activities efficiently on daily basis environmental changes. Over the past four decades, Neurospora crassa has been developed as a model organism for the study of circadian clocks. However, despite the intensive molecular characterizations of the Neurospora circadian clock, our understanding of this system is far from comprehensive. Quantitative Trait Loci (QTL) analyses, using natural strains, have been successfully utilized over the past decade to dissect complex traits down to a naturally occurring polymorphism that is relevant to phenotypic variations. The high quality genomic sequence and sophisticated molecular biology tools, in combination with the QTL analysis, may make it possible to increase the understanding of mechanisms of circadian regulation and may also provide insights into the biological role of the circadian clock, especially in the process of adapting to local environments, a topic that is somewhat overlooked in current research. In this work, I have explored an alternative strategy to uncover new perspectives in the Neurospora circadian clock. My research has laid the groundwork for QTL analysis and has demonstrated QTL analysis of the clock phenotypes, period and entrained phase using natural populations. In chapter II, I describe the computational, statistical and genetic analyses performed to evaluate the marker potential of Neurospora simple sequence repeat (SSR) and to investigate the biological role of the SSR In chapter III, I describe the research regarding the development of two important bioinformatic tools which include 1) a genetic marker management system which facilitates QTL analysis and subsequent positional cloning steps, and 2) an automatic image processing system for the Neurospora circadian clock phenotype. Lastly, in chapter IV, I describe the results of QTL analysis for the two clock phenotypes (period, phase) in three natural F1 populations using two independent statistical methods. Subsequently, I confirmed the QTL effects of one of those in the BC4 generation which were predicted from the F1 populations by constructing near isogenic lines (NIL).