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By early 2026, it is known that almost 1500 Croatian genetic genealogical samples have Y-DNA haplogroup results from FTDNA and related companies. Out of them, at least 1000 are from Croatia. We can conclude that Croats from Croatia (n=1000) have about 42.3% I2, 25.3% R1a, 8.9% E, 7.6% R1b, 6.8% J2, 4.9% I1, 1.6% G, 1% Q, and others <1%. The haplogroup frequencies are almost identical and confirm the percentages in Mršić et al. 2012 (n=1100) and Primorac et al. 2022 (n=518). Croats in Bosnia and Herzegovina (n=320) have about 57.5% I2, 17.19% R1a, 10.31% E, 6.25% I1, 3.44% R1b, 2.81% J2, 1.25% G, and traces of the rest. In subregional frequencies, there are differences, for example in BiH, in the haplogroup I2 between Bosnia (~50%) and Tropolje and Herzegovina (>63%), and in the haplogroup R1a between Bosnia and Tropolje (>23%) compared to Herzegovina (~10%).
Haplogroup I2 (link) is almost exclusively represented by Slavic lineage I2a-L460 > P37.2 > M423 > L621 > CTS10228 > Y3120/S20602 (95%), of which I-Y3548/S17250 > PH908 subclades make up on average 60-70% of it and the rest are I-BY128/Y5596, I-Z17855, I-Y4882, I-Y4460, I-FT76511, and I-FT270447, among others. In the other I2 macroclades, which are basically pre-Slavic, there are I2a-L460 > M436 > M223 > (> P78, S2361, Y3259), I2a-P37.2 > CTS595 > L233 and M26, and least I2a-M436 > L38 > S2906 and I2c-L596 > S6687, all of these subclades are very rare and out of 420 I2 samples with the basic phylogenetic sequence, there are less than 5% (20/420) or 2% overall (20/1000).
Haplogroup R1a (link) is also of Slavic origin and represented predominantly by R1a-M558/CTS1211 (80%), with a minority of R1a-M458, and very rarely R1a-Z92, and R1a-Z93 (this one of probable Hunnic-Avar origin). In R1a-M558/CTS1211, the vast majority of samples are positive for the clade R1a-YT35 > CTS3402, and much less for R1a-Y35 > L1280 > Y5647, R1a-Y2205 > YP343 > YP340 > YP371 and P278.2. In R1a-CTS3402, the majority are positive for R1a-Y2613 (> Y2608), and the rest are R1a-Y33 > Y2902/Y1392, R1a-YP237 > YP953 > YP951, R1a-YP237 > YP295 > L366, and so on. In R1a-M458, the majority is R1a-L260 with subclades R-YP1337, R-Y2905, and R-YP256 > YP654, and the minority is R1a-L1029, which is confirmed to be subclade R-YP417 with other potentially unrelated.
Haplogroup E is almost exclusively E-V13, with individual exceptions being E-M34>Z21467/Y29061 and E-M84. In E-V13, the predominant subclade is E-CTS1273 > BY3880 with its subclades.
Haplogroup R1b is almost exclusively R1b-L23, with two individual exceptions being R1b-PF7562. The macroclade R1b-L23 splits into a West Germanic majority > L51, and an Old Balkan minority > Z2103. R1b-L51 splits into > U152 (majority > L2 (> Z49 > S8183) and a minority > Z193), > L151 (majority > U106 and a minority > DF19 and DF27), > L52 (> L21 > D63, DF13) and a minority > L48.
Haplogroup J2 is divided into half J2b-M241 > L283 (Illyrian) and half J2b-M205 (with some CTS1969 > PH4306 > Y22059), and others are in rare J2a-L26 > M67, L25, L27, L24, M319 clades.
Haplogroup I1 is divided into several subclades, most notably I-Z63, I-Z2336 > P109 (probably > FGC22045), I-58, I-DF29, I-Y3549/Z2338, I-Z60. Within I-Z63 are subclades > Y6228, BY322, FGC9550, Y7075.
Haplogroup G is predominantly G2a (> P15 > L30 > CTS574 > L497; CTS574 > M406; less frequently P15 > L166, Z6700), and a minority is G1a (> M342 > BY1124, CTS11562).
Haplogroup Q is predominantly Q2a (> M378 > L245 > Y2209 > BZ3000), with a minority of Q1b (> L472 > L56 and L713).
Haplogroup T is exclusively T1a-M70 which divides into > L131 > L446 > usually Y6055 and into > L208 > CTS11451, Y16897.
Haplogroup J1 is more J1a > M267 > L136 > P58 and less L137 > PF7263/ZS4416.
Haplogroup N is N-P189.2 (assumed subclade > FT182494), and according to Y-SNP scientifically tested Croatian populations, there should be the N-TAT clade, or both simply absent, depending on the tested population.
The current ancient DNA database contains 465 samples; of these, around 200 have Y-DNA haplogroup assignments, and 395 have mtDNA haplogroup assignments. There's no Y-DNA sample for the Mesolithic Age, but considering the Iron Gates Mesolithic archaeological culture from eastern Serbia and western Romania, it could be considered that the predominantly present haplogroups were I2a-L460, C-F3393, and R1b1a-L754, which are typical of Western or Eastern European hunter-gatherers. In the Neolithic Age, Anatolian Neolithic farmers arrived, assimilated previous populations, and were predominantly represented by haplogroup G2a (43%) with some C (25%) and I2 (18%), and a few early E1b1b and J2a. The predominance of G2a (68%) and the top three haplogroup combinations persisted in the Neolithic and Chalcolithic Age, and the mentioned haplogroup I2 was represented only by I2-M223, I2-L596, and I2-P37.2>CTS595>L1286 clades, but the I2 almost vanished in subsequent ages.
In the Bronze Age, a large-scale migration and conquest of Europe by the Indo-Europeans, seen with predominance of R1b (33%) and J2b (47%), and diminishing of a still significant minority of G2a (16%). In the Iron Age became even more predominant (66%) haplogroup J2b(-L283) specifically related to the Illyrians. With their downfall and conquest by the Romans, the population's paternal genetic heritage became very heterogeneous, with J2b diminishing to 22% and the rise of J2a (17%), E1b1b (15%), and the appearances of barbarian I1, R1a(-Z93), and N. In the early medieval period, the genetic landscape changed drastically once again, with the arrival of the early Slavs. Most prominent haplogroups became I2-M423(>CTS10228>Y3120) and R1a, which persisted and rose until the modern age, while Illyrian J2b(>L283) almost vanished.