Abstract: The marker regression and the interval mapping methods were used for the detection of qualitative trait loci (QTL) in Arabidopsis thaliana in a cross between early flowering ecotypes Landsberg erecta and Columbia. The interval mapping method employs pairs of neighbouring markers to obtain maximum linkage information about the presence of a QTL within the enclosed segment of the chromosome, whereas the marker regression approach fits a model to all the marker means on a given chromosome simultaneously and obtains significance tests by simulation. The interval mapping method detected 22 QTL in seven traits and the marker regression method detected 22 QTL in six traits. The two methods detected sixteen QTL at similar positions of the Arabidopsis chromosomes and QTL for similar traits were localised to similar regions of the chromosomes and they showed similar mode of additive effect. This suggested that the two methods are similar in their QTL detection even though they employed different significant levels.