In this paper the well-known non-random associations between Lap and Pept-1 loci and gene arrangements of chromosome O are studied in laboratory populations of D. subobscura. An increase of the frequency of the allele Lap1.00, towards an equilibrium point (0.70), was found to be associated with an increase of the gene arrangement O3+4. This is an accordance to the associations found in natural populations. On the contrary no such an increase was observed in populations polymorphic for Lap and Pept-1 loci but homokaryotypic for gene arrangement O3+4+8 differing in the initial allele frequencies at these loci. Although epistatic selection cannot be completely ruled out, our results are better explained under the assumption of neutrality.