This is a first attempt towards a detailed understanding of malacofaunna of Faisalabad Pakistan. The present study has been carried out on the morphometric and molecular characterization and genetic diversity of snails in the agroecosystem of Faisalabad City from March 2011 through August 2011. During this period 19290 snails were randomly collected from four agroecosystems (sugarcane, wheat, fodder, vegetables fields) and ditches from villages linked with Rakh branch, Jhang branch and Ghogera branch. The snails were isolated from the soil samples through sifting through screen of mesh size less than 1 mm. The snail specimens were studied under the microscope. The snail species were identified by using recent identification keys i.e., Blandford and Godwin (1908), Bouchet and Rocroi (2005), Sturm et al., (2005), Anderson, (2008), Watson and Dallwitz (2005) and diagrammatic description provided in them. The identification of the specimens was made on the basis of number of whorls, coiling of the shell, umbilicus, shape, colour, shape of the aperture, presence or absence of operculum, height (mm), diameter (mm), and the diameter of the aperture (mm) using vernier caliper. The snails were found belonging to two suborders, seven families, nine genera, fifteen species out of which six species have been reported first time in this region. Molecular characterization of snails has been done with the help of randomly amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) technique for understanding the biodiversity in this region. Genetic characterization of 15 snail species was done by using 23 RAPD primers and out of which 15 RAPD primers produced polymorphic amplification. On the basis of Analysis of Molecular Variance there was found 11% variation among populations of the five habitats and 89% variation within populations in species population found in all the habitats. Genetic similarity among snail species was estimated by Nei’s genetic similarity indices showing a range of 0.5 to 0.74. Maximum genetic similarity was found between Ariophanta belangeri bombayana and Ariophanta bristrialis taprobanensis as well as Ariophanta belangeri bombayana and Ariophanta solata. Minimum genetic similarity based on Nei’s genetic indices was observed among Cernuella virgata and Ariophanta bistrialis cyix. Considering the Zooctecus insularis and Juvenile Zooctecus insularis they are quite distant from each other in the cluster due to which it is expected that might belong to some new species, which need further investigations. The data of distribution and abundance was subject to different statistical tools i.e., shannon and wienerdiversity index, index of overall association, two way analysis of variance, multiple regression, cluster analysis shows that as we progress towards south, the diversity of the snail species in Faisalabad is highly reduced. However the species diversity in all the villages linked to R.B., G.B. and J.B. was highly significant with a strong positive relationship between species diversity and species evenness (97.03%). The diversity indices in all the habitats of the agroecosystem were highly significant while in ditches the results were non-significant with a strong negative correlation between species diversity and evenness in the crops that clearly shows that when diversity is low the evenness was high and viceversa in the distribution of snails in the different crops. There is 95.3% relationship between species diversity and species evenness in different crops of Faisalabad. The species diversity is highly significant in all the months except in April.Regression analysis between species diversity and species evenness shows that there is 57.36% relationship between them in different months in agroecosystem of Faisalabad. There is a significant effect of maximum and minimum temperatature on the number of snails while other abiotic factors i.e., humidity, rainfall, sunshine, soil cadmium concentration, soil lead concentration, soil pH, soil electrical conductivity has a non-significant effect on them. The soil parameters have been found much less than National envoirnmental quality standards Pakistan. However the association between the species and months and between species and agroecosystem has been found highly significant. Interspecific association indices suggests an overall positive association however no association has been found during different months while a strong association has been found with different habitats.This study has given us a baseline data of the malacofaunna in Faisalabad which will help us to identify the indicator species, develop ecological models, and conservation strategies by the policy makers.