Fifty-three isolines of Anopheles peditaeniatus were established from individual wild-caught females collected from cow-baited traps in 17 provinces of Thailand. Three types of X (X1, X2, X3) and 6 types of Y (Y1,Y2, Y3, Y4, Y5, Y6) chromosomes were determined based on different amounts of major block(s) of heterochromatin. These sex chromosomes comprised 6 karyotypic forms designated as Forms A (X3, Y1), B (X1, X2, X3, Y2), C (X3, Y3), D(X1, X2, X3, Y4), E (X1, X2, X3,Y5) and F (X2, X3, Y6). Form F is a new metaphase karyotype discovered in this study and is commonly found in all regions. Form A was found only in Lampang province, whereas Form E is widespread throughout the country. Forms B, C and D were obtained from the northern, northeastern, western and southern regions. Crossing experiments among the 11 isoline colonies representing the 6 karyotypic forms of An. peditaeniatus indicated genetic compatibility yielding viable progenies and complete synapsis of salivary gland polytene chromosomes through to the F2-generations. The results suggested the conspecific nature of these karyotypic forms which were further supported by very low intraspecific variation (genetic distance = 0.000-0.003) of nucleotide sequences in ribosomal DNA (ITS2) and mitochondrial DNA (COI and COII).