The fatty acid synthase (FASN) gene codes for a multifunctional protein, catalyzing the de novo fatty acid synthesis. Its high mRNA expression in GMEC (goat mammary epithelial cells), coinciding with medium to high heritability of milk fat, substantiated its role as a candidate gene for association analysis with milk fat profile. The main objectives of the study were to develop markers of Capra hircus FASN gene to improve healthfulness of goat milk FAs (fatty acids) and to investigate early lactation milk fat profile. A Linear mixed model association analysis of 46 dependent variables, analyzed from 300 milk samples 30 d postpartum, with 3 intragenic SNPs and 2 haplotype groups was conducted. The results had revealed associations of FASN SNPs and haplotype groups with myristic acid (C14:0), palmitic acid (C16:0) and linoleic acid (C18:2 n-6, cis). Herd was the predominant factor affecting fatty acid levels followed by herd-test-day (HTD) and parity, indicating the niche of nutrition and management in modulating early lactation milk fat profile. De novo FAs (C6:0 to C14:0) showed suppressed levels with strong negative correlations with C18 FAs. Contradicting to the presumed source of origin, butyric acid (C4:0) was impervious to the observed de novo FA depression, it had shown unique correlation patterns. Oleic acid (C18:1 cis-9) scored the highest mean value followed by palmitic acid. Palmitic acid had shown normal levels with weak negative correlations with C6:0 and C8:0. Here, its dual source of origin supposedly had played a role, in replenishing the diminished levels of de novo contribution, by the high C16 FAs bioavailability of body fat mobilization, which masked the inhibitory effect of long chain FAs. The correlation patterns of odd chain FAs with CLA and rumen derived biohydrogenation intermediates reinforce the supposition that odd chain fatty acids could serve as a diagnostic tool of rumen condition and biohydrogenation patterns. The SNP markers developed in the present study will assist in marker assisted selection, and the comprehensive analysis of early lactation milk fat profile will help to decipher main factors of variation, thereby aiding fatty acid profile modulation.